A structure-controlled investigation of lipase enantioselectivity by a path-planning approach

A novel approach based on efficient path-planning algorithms was applied to investigate the influence of substrate access on Burkholderia cepacia lipase enantioselectivity. The system studied was the transesterification of 2-substituted racemic acid derivatives catalysed by B. cepacia lipase. In silico data provided by this approach showed a fair qualitative agreement with experimental results, and hence the potential of this computational method for fast screening of racemates. In addition, a collision detector algorithm used during the pathway searches enabled the rapid identification of amino acid residues hindering the displacement of substrates along the deep, narrow active-site pocket of B. cepacia lipase and thus provided valuable information to guide the molecular engineering of lipase enantioselectivity.     

Bioinformatics-driven, rational engineering of protein thermostability

A longstanding goal in protein engineering is to identify specific sequence changes that endow proteins with desired functional properties. As opposed to traditional rational and random protein engineering techniques, we have employed a bioinformatic approach to identify specific sequence changes that influence key functional properties of a protein within a defined superfamily. Specifically, we have used the Bayesian sequence-based algorithms PROBE and Classifier to identify a strand-turn-strand motif that contributes to thermophilicity among members of the serine protease subtilase superfamily. By replacing a 16 amino acid sequence in the mesophilic subtilisin E (from Bacillus subtilis) with a bioinformatics-generated thermophilic model sequence, the melting temperature of subtilisin E was increased by 13 degrees C. While wild-type subtilisin E was inactive at 90 degrees C, the mutant retained a substantial fraction of its function, with ca. one-third of the activity that it has at 45 degrees C.     

Pseudomonas glumae lipase: increased proteolytic stabifity by protein engineering

The feasibility of stabilizing proteins towards proteolyticdegradation was explored by engineering the primary proteolyticcleavage site(s). This novel approach does not require informationon the 3-D structure of the native enzyme. As a model system,the extracellular lipase of Pseudomonas glumae was chosen, whichis sensitive towards degradation by subtilisin-tvpe proteases.The primary proteolytic cleavage in the lipase appeared to belocated between amino acids serine 153 and histidine 154. SincesubtUisins are known to show a preference towards amino acidresidues surrounding the scissile bond, non-preferred aminoadds were introduced in this area. Two concepts were tested:the introduction of arginine or glutainate residues (chargeconcept) and the introduction of proline residues (proUne concept).Although the mutant Upases produced according to either of theseconcepts were still cleaved in the same area, they showed aconsiderably increased stability towards proteolytic degradation.     

A novel genetic selection system for improved enantioselectivity of Bacillus subtilis lipase A

In directed evolution experiments, success often depends on the efficacy of screening or selection methods. Genetic selections have proven to be extremely valuable for evolving enzymes with improved catalytic activity, improved stability, or with altered substrate specificity. In contrast, enantioselectivity is a difficult parameter to select for. In this study, we present a successful strategy that not only selects for catalytic activity, but for the first time also for enantioselectivity, as demonstrated by the selection of Bacillus subtilis lipase A variants with inverted and improved enantioselectivity. A lipase mutant library in an aspartate auxotroph Escherichia coli was plated on minimal medium that was supplemented with the aspartate ester of the desired enantiomer (S)-(+)-1,2-O-isopropylidene-sn-glycerol. To inhibit growth of less enantioselective variants, a covalently binding phosphonate ester of the opposite (R)-(-)-1,2-O-isopropylidene-sn-glycerol enantiomer was added as well. After three selection rounds in which the selection pressure was increased by raising the phosphonate ester concentration, a mutant was selected with an improved enantioselectivity increased from an ee of -29.6 % (conversion 23.4 %) to an ee of +73.1 % (conversion 28.9 %) towards the (S)-(+)-enantiomer. Interestingly, its amino acid sequence showed that the acid of the catalytic triad had migrated to a position further along the loop that connects beta7 and alphaE; this shows that the position of the catalytic acid is not necessarily conserved in this lipase.     

Creating space for large secondary alcohols by rational redesign of Candida antarctica lipase B

The active site of Candida antarctica lipase B (CALB) hosts the catalytic triad (Ser-His-Asp), an oxyanion hole and a stereospecificity pocket. During catalysis, the fast-reacting enantiomer of secondary alcohols places its medium-sized substituent in the stereospecificity pocket and its large substituent towards the active-site entrance. The largest group to fit comfortably in the stereospecificity pocket is ethyl, and this restricts the number of secondary alcohols that are good substrates for CALB. In order to overcome this limitation, the size of the stereospecificity pocket was redesigned by changing Trp104. The substrate specificity of the Trp104Ala mutant compared to that of the wild-type lipase increased 270 times towards heptan-4-ol and 5500 times towards nonan-5-ol; this resulted in the high specificity constants 1100 and 830 s(-1) M(-1), respectively. The substrate selectivity changed over 400,000 times for nonan-5-ol over propan-2-ol with both Trp104Ala and the Trp104Gln mutations.     

Learning from directed evolution: theoretical investigations into cooperative mutations in lipase enantioselectivity

Molecular modeling with classical force-fields has been used to study the reactant complex and the tetrahedral intermediate in lipase-catalyzed ester hydrolysis in 20 enzyme/substrate combinations. The R and S enantiomers of alpha-methyldecanoic acid ester served as substrates for the wild-type lipase from Pseudomonas aeruginosa and nine selected mutants. After suitable preparation of initial structures from an available wild-type crystal structure, each system was subjected to 1 ns CHARMM force-field molecular dynamics simulations. The resulting geometric and energetic changes allow interpretation of some experimentally observed effects of mutations, particularly with regard to the "hot spots" at residues 155 and 162. The replacement S155F enhances S enantiopreference through a steric relay involving Leu162. The double mutation S53P + L162G improves S enantioselectivity by creating a new binding pocket for the S enantiomer with an additional stabilizing hydrogen bond to His83. The simulations provide insight into remote and cooperative effects of mutations.     

Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A

The prospect for consistent computer-aided refinement of stereoselective enzymes is explored by simulating the hydrolysis of enantiomers of an α-substituted ester by wild-type and mutant Candida antarctica lipase A, using several strategies. In particular, we focused on the use of the empirical valence bond (EVB) method in a quantitative screening for enantioselectivity, and evaluate both k(cat) and k(cat)/K(M) of the R and S stereoisomers. We found that an extensive sampling is essential for obtaining converging results. This requirement points towards possible problems with approaches that use a limited conformational sampling. However, performing the proper sampling appears to give encouraging results and to offer a powerful tool for the computer-aided design of enantioselective enzymes. We also explore faster strategies for identifying mutations that will help in augmenting directed-evolution experiments, but these approaches require further refinement.     

Polar order by rational design: crystal engineering with parallel beloamphiphile monolayers

Polar order in the biosphere is limited to nanometer-sized domains, occurs with essentially complete cancellation, or is avoided on purpose. One thus wonders whether large-scale polar order is even possible, and this question is the subject of the dipole alignment problem. We addressed this challenge with an interdisciplinary approach bringing together elements of mathematics, electronic structure theory and computational chemistry, physical-organic and synthetic chemistry, crystallization and crystallography, and, most importantly, patience and much thought about intermolecular bonding in molecular crystals. The azine- and biphenyl-based beloamphiphiles (Y-Ph-MeC=N-N=CMe-Ph-X and Y-Ph-Ph-X) are ascendants of a new generation of highly anisotropic functional materials with perfect polar order.     

The creation of a novel fluorescent protein by guided consensus engineering

Consensus engineering has been used to increase the stability of a number of different proteins, either by creating consensus proteins from scratch or by modifying existing proteins so that their sequences more closely match a consensus sequence. In this paper we describe the first application of consensus engineering to the ab initio creation of a novel fluorescent protein. This was based on the alignment of 31 fluorescent proteins with >62% homology to monomeric Azami green (mAG) protein, and used the sequence of mAG to guide amino acid selection at positions of ambiguity. This consensus green protein is extremely well expressed, monomeric and fluorescent with red shifted absorption and emission characteristics compared to mAG. Although slightly less stable than mAG, it is better expressed and brighter under the excitation conditions typically used in single molecule fluorescence spectroscopy or confocal microscopy. This study illustrates the power of consensus engineering to create stable proteins using the subtle information embedded in the alignment of similar proteins and shows that the benefits of this approach may extend beyond stability.     

Improved activity and thermostability of Candida antarctica lipase B by DNA family shuffling

DNA family shuffling was used to create chimeric lipase B proteins with improved activity toward the hydrolysis of diethyl 3-(3',4'-dichlorophenyl)glutarate (DDG). Three homologous lipases from Candida antarctica ATCC 32657, Hyphozyma sp. CBS 648.91 and Crytococcus tsukubaensis ATCC 24555 were cloned and shuffled to generate a diverse gene library. A high-throughput screening assay was developed and used successfully to identify chimeric lipase B proteins having a 20-fold higher activity toward DDG than lipase B from C.antarctica ATCC 32657 and a 13-fold higher activity than the most active parent derived from C.tsukubaensis ATCC 24555. In addition, the stability characteristics of several highly active chimeric proteins were also improved as a result of family shuffling. For example, the half-life at 45 degrees C and melting point (T(m)) of one chimera exceeded those of lipase B from C.antarctica ATCC 32657 by 11-fold and 6.4 degrees C, respectively, which closely approached the stability characteristics of the most thermostable parent derived from Hyphozyma sp. CBS 648.91.     

Learning from directed evolution: Further lessons from theoretical investigations into cooperative mutations in lipase enantioselectivity

An earlier experimental study, which involved the directed evolution of enantioselective lipase variants from Pseudomonas aeruginosa as catalysts in the hydrolytic kinetic resolution of 2-methyl-decanoic acid p-nitrophenyl ester, provided a mutant with six mutations. Consequently, the selectivity factor was found to increase from E = 1.1 for the wild-type to E = 51 for the best mutant. Only one of the amino acid exchanges in this mutant was found to occur next to the binding pocket, the other mutations being remote. Our previous theoretical analysis with molecular-dynamics simulations helped to unveil the source of enhanced enantioselectivity: a relay mechanism that involves two of the six mutations was shown to induce strong cooperativity. In this investigation, single, double, and triple mutants were constructed and tested as enantioselective catalysts. This study supports our original postulate regarding the relay mechanism, offers further mechanistic insight into the role of individual mutations, and provides mutants that display even higher enantioselectivity (E of up to 64).     

基于化学修饰法探讨脂肪酶对手性伯醇的识别机理

洋葱假单胞菌脂肪酶（PcL）催化多种手性伯醇酯的不对称水解反应显示其对结构中含有额外的非酯键氧原子的手性伯醇酯的对映体选择性较高,而对不含额外氧原子的选择性差。分别用多种氨基酸残基特异性的修饰剂修饰 PcL,结果发现经 N-乙酰咪唑（NAI）修饰酪氨酸残基（Tyr）后 PcL 对含额外非酯键氧原子的手性伯醇酯对映体选择性显著降低,而对不含额外氧的伯醇酯选择性几乎不受影响。蛋白质谱证实产生主要影响的是位于 PcL 活性口袋内的 Tyr29 残基,手性伯醇酯能否与 Tyr29 形成额外氢键决定了 PcL对其选择性。分子动力学模拟表明,Tyr29被修饰的 PcL 不能与底物形成氢键,因此选择性明显下降。这一发现成功揭示了脂肪酶对手性伯醇对映体选择性的分子识别机理。     

A water molecule in the stereospecificity pocket of Candida antarctica lipase B enhances enantioselectivity towards pentan-2-ol

The effect of water activity on enzyme-catalyzed enantioselective transesterification was studied by using a solid/gas reactor. The experimental results were compared with predictions from molecular modelling. The system studied was the esterification of pentan-2-ol with methylpropanoate as acyl donor and lipase B from Candida antarctica as catalyst. The data showed a pronounced water-activity effect on both reaction rate and enantioselectivity. The enantioselectivity increased from 100, at water activity close to zero, to a maximum of 320, at a water activity of 0.2. Molecular modelling revealed how a water molecule could bind in the active site and obstruct the binding of the slowly reacting enantiomer. Measurements of enantioselectivity at different water-activity values and temperatures showed that the water molecule had a high affinity for the stereospecificity pocket of the active site with a binding energy of 9 kJ mol-1, and that it lost all its degrees of rotation, corresponding to an entropic energy of 37 J mol-1 K-1.     

Mapping the folding pathway of the transmembrane protein DsbB by protein engineering

The four-helical transmembrane protein DsbB (disulfide bond reducing protein B) folds and unfolds reversibly in mixed anionic/non-ionic micelles, consisting of an unfolding intermediate I and a rate-limiting transition state (TS) between I and the denatured state D. Here, I describe the analysis of the folding behavior of 12 different alanine-scanning mutants of DsbB. For all mutants, TS is as compact as D and there is an accelerating increase in compaction as the protein proceeds to I and the native state. This unusual pattern of consolidation may reflect significant amounts of secondary structure in D, analogous to a classical folding intermediate. Unexpectedly, an increase in apolar surface area upon mutation is stabilizing whereas an increase in polar surface area is destabilizing. This effect is probably dominated by the effect of the mutations on the structure of the denatured state. I observe clear Hammond postulate behavior, in which a destabilization of I moves it closer to D. Φ-Value analysis indicates that in TS, a folding nucleus consisting of two to three residues with Φ-values of > 0.5 forms at one end of the transmembrane helices, which expands to include residues closer to the middle of the protein in I. Thus, folding proceeds from a highly polarized starting point.     

Increased proteolytic resistance of ribonuclease A by protein engineering

Although highly stable toward unfolding, native ribonucleaseA is known to be cleaved by unspecific proteases in the flexibleloop region near Ala20. With the aim to create a protease-resistantribonuclease A, Ala20 was substituted for Pro by site-directedmutagenesis. The resulting mutant enzyme was nearly identicalto the wild-type enzyme in the near-UV and far-UV circular dichroismspectra, in its activity to 2',3'-cCMP and in its thermodynamicstability. However, the proteolytic resistance to proteinaseK and subtilisin Carlsberg was extremely increased. Pseudo-first-orderrate constants of proteolysis, determined by densitometric analysisof the bands of intact protein in SDS–PAGE, decreasedby two orders of magnitude. In contrast, the rate constant ofproteolysis with elastase was similar to that of the wild-typeenzyme. These differences can be explained by the analysis ofthe fragments occurring in proteolysis with elastase. Ser21–Ser22was identified as the main primary cleavage site in the degradationof the mutant enzyme by elastase. Obviously, this bond is notcleavable by proteinase K or subtilisin Carlsberg. The resultsdemonstrate the high potential of a single mutation in proteinstabilization to proteolytic degradation.     

Quick analysis of enantioselectivity by a chromatographic reactor: II. Experimental verification

A modified chromatographic process was used to determine the enantiomeric ratio (E) in enantioselective biocatalysis. Theoretical results indicated that the established relationship, E = ln(1−x^S)/ln(1−x^R), was valid for this modified operation. In addition, the Candida cylindracea lipase‐catalyzed enantioselective esterification of racemic naproxen was selected to verify experimentally the effectiveness of the proposed method. The ease of operation and simplicity of data analysis of the proposed method makes it a promising alternative for determining the enantioselectivity of enzymatic chiral resolution. © 1999 Society of Chemical Industry     

A system of deformation data for rational engineering design with plastics

The paper discusses the deformational behaviour of thermoplastics, particularly in relation to their utilization through rational engineering design procedures. It describes the comprehensive systems of data that are replacing the old single datum quantities published hitherto and comments briefly on the corrdination of materials testing through the activities of B.S.I. Committee PLC/36.     

Rational stabilization of the C-LytA affinity tag by protein engineering

The C-LytA protein constitutes the choline-binding module of the LytA amidase from Streptococcus pneumoniae. Owing to its affinity for choline and analogs, it is regularly used as an affinity tag for the purification of proteins in a single chromatographic step. In an attempt to build a robust variant against thermal denaturation, we have engineered several salt bridges on the protein surface. All the stabilizing mutations were pooled in a single variant, C-LytAm7, which contained seven changes: Y25K, F27K, M33E, N51K, S52K, T85K and T108K. The mutant displays a 7 degrees C thermal stabilization compared with the wild-type form, together with a complete reversibility upon heating and a higher kinetic stability. Moreover, the accumulation of intermediates in the unfolding of C-LytA is virtually abolished for C-LytAm7. The differences in stability become more evident when the proteins are bound to a DEAE-cellulose affinity column, as most of wild-type C-LytA is denatured at approximately 65 degrees C, whereas C-LytAm7 may stand temperatures up to 90 degrees C. Finally, the change in the isoelectric point of C-LytAm7 enhances its solubility at acidic pHs. Therefore, C-LytAm7 behaves as an improved affinity tag and supports the engineering of surface salt bridges as an effective approach for protein stabilization.     

Hydrolysis of soybean oil by a combined lipase system

The hydrolysis of soybean oil by different lipases was compared, and the results demonstrated that lipases D, N and G hydrolyzed the oil to 44, 42 and 7.2%, respectively, after 10 hr reaction, which represents incomplete hydrolysis. But the combined enzyme systems (lipases (G+N and lipases G+D) hydrolyzed the oil to an extent of 95–98% after 10 hr reaction. Plotting the percentage hydrolysis of soybean oil by combined enzyme systems against the logarithm of the reaction time resulted in essentially straight lines.