Control of Subtilisin Substrate Specificity by Solvent Engineering in Organic Solvents and Supercritical Fluoroform

Evolving Robust and Interpretable Enzymes for the Bioethanol Industry

Obtaining a robust and applicable enzyme for bioethanol production is a dream for biorefinery engineers. Herein, we describe a general method to evolve an all-round and interpretable enzyme that can be directly employed in the bioethanol industry. By integrating the transferable protein evolution strategy InSiReP 2.0 (In Silico guided Recombination Process), enzymatic characterization for actual production, and computational molecular understanding, the model cellulase PvCel5A (endoglucanase II Cel5A from Penicillium verruculosum) was successfully evolved to overcome the remaining challenges of low ethanol and temperature tolerance, which primarily limited biomass transformation and bioethanol yield. Remarkably, application of the PvCel5A variants in both first- and second-generation bioethanol production processes (i. Conventional corn ethanol fermentation combined with the in situ pretreatment process; ii. cellulosic ethanol fermentation process) resulted in a 5.7-10.1 % increase in the ethanol yield, which was unlikely to be achieved by other optimization techniques.

Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents

Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.

Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance

Biocatalysis for the synthesis of fine chemicals is highly attractive but usually requires organic (co-)solvents (OSs). However, native enzymes often have low activity and resistance in OSs and at elevated temperatures. Herein, we report a smart salt bridge design strategy for simultaneously improving OS resistance and thermostability of the model enzyme, Bacillus subtilits Lipase A (BSLA). We combined comprehensive experimental studies of 3450 BSLA variants and molecular dynamics simulations of 36 systems. Iterative recombination of four beneficial substitutions yielded superior resistant variants with up to 7.6-fold (D64K/D144K) improved resistance toward three OSs while exhibiting significant thermostability (thermal resistance up to 137-fold, and half-life up to 3.3-fold). Molecular dynamics simulations revealed that locally refined flexibility and strengthened hydration jointly govern the highly increased resistance in OSs and at 50-100 °C. The salt bridge redesign provides protein engineers with a powerful and likely general approach to design OSs- and/or thermal-resistant lipases and other α/β-hydrolases.

Chemoenzymatic synthesis of polypeptides in neat 1,1,1,2-tetrafluoroethane solvent

Chemoenzymatic polypeptide synthesis offers several advantages over chemical or other biological routes, however, the use of aqueous-based media suffers from reverse hydrolysis reactions that challenge peptide chain propagation. Herein, the protease from subtilisin Carlsberg biocatalyzed the synthesis of poly-l-PheOEt, poly-l-LeuOEt, and the copolymers poly-l-PheOEt-co-l-LeuOEt from their amino acid ethyl ester substrates in a neat liquid 1,1,1,2-tetrafluoroethane solvent. The products, achieved in acceptable yields (ca. 50%), were fully characterized showing relatively high molar mass (ca. 20 000 Da for poly-l-PheOEt). This non-toxic low-boiling hydrofluorocarbon enhances enzymatic peptide propagation by limiting hydrolysis owing to its hydrophobic and relatively polar characteristics that sustain the protease activity and solubilize substrates and products. Computational molecular dynamic calculations were used to assess the l-PheOEt/l-LeuOEt-solvent and polypeptide-solvent interactions in this system. Additionally, the homopolypeptides displayed higher crystallinity than the copolypeptides with random incorporation of amino acid ethyl esters, notwithstanding the significantly highest specificity for Phe in this system. Interestingly, secondary structure characterization of the products by FTIR and circular dichroism suggests a non-common peptide folding.

Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media

In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.

High pressure CO2-controlled reactors: enzymatic chiral resolution in emulsions

Chiral separation of ibuprofen catalyzed by enzyme conducted in CO₂-based micelle makes the reaction more effective and greener.

Nonthermal effect of microwave irradiation in nonaqueous enzymatic esterification

Microwave has nonthermal effects on enzymatic reactions, mainly caused by the polarities of the solvents and substrates. In this experiment, a model reaction with caprylic acid and butanol that was catalyzed by lipase from Mucor miehei in alkanes or arenes was employed to investigate the nonthermal effect in nonaqueous enzymatic esterification. With the comparison of the esterification carried by conventional heating and consecutive microwave irradiation, the positive nonthermal effect on the initial reaction rates was found substrate concentration-dependent and could be vanished ostensibly when the substrate concentration was over 2.0 mol L(-1). The polar parameter log P well correlates the solvent polarity with the microwave effect, comparing to dielectric constant and assayed solvatochromic solvent polarity parameters. The log P rule presented in conventional heating-enzymatic esterification still fits in the microwaved enzymatic esterification. Alkanes or arenes with higher log P provided positive nonthermal effect in the range of 2 ≤ log P ≤ 4, but yielded a dramatic decrement after log P = 4. Isomers of same log P with higher dielectric constant received stronger positive nonthermal effect. With lower substrate concentration, the total log P of the reaction mixture has no obvious functional relation with the microwave effect.

Solvent as a competitive inhibitor for Candida antarctica lipase B

In enzyme-catalyzed reactions, the choice of solvent often has a marked effect on the reaction outcome. In this paper, it is shown that solvent effects could be explained by the ability of the solvent to act as a competitive inhibitor to the substrate. Experimentally, the effect of six solvents, 2-pentanone, 3-pentanone, 2-methyl-2-pentanol, 3-methyl-3-pentanol, 2-methylpentane and 3-methylpentane, was studied in a solid/gas reactor. As a model reaction, the CALB-catalyzed transacylation between methyl propanoate and 1-propanol, was studied. It was shown that both ketones inhibited the enzyme activity whereas the tertiary alcohols and the hydrocarbons did not. Alcohol inhibition constants, K(i)(I) were changed to "K(i)", determined in presence of 2-pentanone, 3-pentanone, and 3-methyl-3-pentanol, confirmed the marked inhibitory character of the ketones and an absence of inhibition of 3-methyl-3-pentanol. The molecular modeling study was performed on three solvents, 2-pentanone, 2-methyl-2-pentanol and 2-methyl pentane. It showed a clear inhibitory effect for the ketone and the tertiary alcohol, but no effect for the hydrocarbon. No change in enzyme conformation was seen during the simulations. The study led to the conclusion that the effect of added organic component on lipase catalyzed transacylation could be explained by the competitive inhibitory character of solvents towards the first binding substrate methyl propanoate.

Cytochrome c−Crown Ether Complexes as Supramolecular Catalysts: Cold-Active Synzymes for Asymmetric Sulfoxide Oxidation in Methanol

A series of supramolecular complexes of various cytochrome c proteins with 18-crown-6 derivatives behave as cold-active synzymes in the H2O2 oxidation of racemic sulfoxides. This interesting behavior contrasts with native functionality, where the employed proteins act as electron transfer carriers. ESI-MS. UV, CD, and Raman spectroscopic characterizations reveal that four or five 18-crown-6 molecules strongly bind to the surface of the cytochrome c and also that nonnatural low-spin hexacoordinate heme structures are induced in methanol. Significantly, crown ether complexation can convert catalytically inactive biological forms to catalytically active artificial forms. Horse heart, pigeon breast, and yeast cytochromes c all stereoselectively oxidize (S)-isomers of methyl tolyl sulfoxide and related sulfoxides upon crown ether complexation. These supramolecular catalysts show the highest efficiency and enantiomer selectivity at -40 degrees C in the H202-dependent sulfoxide oxidation, while oxidative decomposition of the heme moieties predominantly occurs at room temperature. The oxidation reactivity of the employed sulfoxides is apparently related to steric constraints and electrochemical oxidation potentials of their S=O bonds. Among the cytochrome c complexes, yeast cytochrome c demonstrates the lowest catalytic activity and degradation reactivity. It has a significantly different protein sequence, suggesting that crown ether complexation effectively activates heme coordination but may additionally alter the native backbone structure. The proper combination of cytochrome c proteins, 18-crown-6 receptors, and external circumstances can be used to successfully generate "protein-based supramolecular catalysts" exhibiting nonbiological reactivities.

Regiospecific alkaline protease-catalyzed divinyl acyl transesterifications of primary hydroxyl groups of mono- and di-saccharides in pyridine

This paper describes highly selective transesterification reactions, catalyzed by an alkaline protease from Bacillus subtilis in pyridine, of several mono- and di-saccharides with divinyl dicarboxylates ranging from 4 to 10 carbon atoms. A series of polymerizable vinyl fatty acid sugar esters were obtained with good selectivity and high yields. Most products had high proportions of the alpha anomer. The influences of the enzymes, solvents, temperature, and acyl donor chain length on the reaction were studied. Vinyl sugar esters offer a new family of functional water-soluble monomers for preparation of sugar-containing polymers.

Chemical activation of cytochrome c proteins via crown ether complexation: cold-active synzymes for enantiomer-selective sulfoxide oxidation in methanol

Supramolecular complexation with 18-crown-6 significantly converted catalytically inactive cytochrome c (biological form) to catalytically active synzyme (artificial form). Although a family of cytochrome c proteins does not work as enzymes in nature, crown ether complexation modified their heme coordination structures and functionally activated them to promote the asymmetric oxidation of racemic sulfoxides at low temperature. Horse heart, pigeon breast, and yeast cytochrome c proteins were demonstrated to form supramolecular complexes with 18-crown-6 in methanol, which effectively oxidized (S)-isomers of naphthyl methyl sulfoxide, methyl tolyl sulfoxide, isopropyl phenyl sulfoxide, benzyl methyl sulfoxide, and 4-methylsulfenyl acetophenone at -40 degrees C. Because horse heart and pigeon breast cytochromes c exhibited more efficient and higher enantiomer-selective activities than yeast cytochrome c, a proper combination of cytochrome c and crown ether offers a new class of cold-active synzymes promoting nonbiological asymmetric oxidation.

Progressive rearrangement of subtilisin Carlsberg into orderly and inflexible conformation with Ca(2+) binding

Fluorescence depolarization and decay kinetic profiles, together with differential scanning calorimetric thermograms and circular dichroism spectra, are measured to understand the respective roles of Ca(2+) ions at the strong (Ca1) and weak binding sites (Ca2) of subtilisin Carlsberg (sC). Thermal denaturation temperature decreases considerably with Ca1 removal, whereas it does slightly with Ca2 removal. The fraction of random coil structure increases significantly with Ca2 removal as well as with Ca1 removal. sC shows three fluorescence decay times of 100, 1100, and 3300 ps. Although the fast and the slow do not change noticeably, the medium one decreases progressively with Ca(2+) removal. sC has two fluorescence anisotropic decay components of 340 and 12,000 ps. The fast one arises from the internal rotation of Tyr, whereas the slow results from the global rotation of sC. Although both become significantly faster with Ca2 removal, only the slow one becomes slightly faster with further Ca1 removal. Overall, sC undergoes progressive rearrangement into disorderly and flexible conformation with Ca(2+) removal, indicating that both Ca1 and Ca2 are indispensable for the stable structure of sC.

Cation-binding sites of subtilisin Carlsberg probed with Eu(III) luminescence

Two Ca(2+)-binding sites of subtilisin Carlsberg are studied by monitoring static and time-resolved luminescence of selectively substituted Eu(3+) at each site, and they are found to be characteristically quite different from each other. Compared with the coordination sphere of free Eu(3+), two sites are very similar to each other, so that both have a well-defined binding structure with low coordination symmetry. However, compared with the weak site, the strong site is relatively more polar, more symmetrical, and more easily accessible. Furthermore, despite the absence of water reported in the x-ray crystal structure (, Eur. J. Biochem. 166:673-692), one water molecule is found to exist in the coordination sphere of the strong site in aqueous solution. Thus it is suggested that in solution the Ca(2+) bound in the strong site forms an additional coordination bond to a solvent or substrate molecule.

Catalytic activity and conformation of chemically modified subtilisin Carlsberg in organic media

Subtilisin Carlsberg, an alkaline protease from Bacillus licheniformis, was modified with polyoxyethylene (PEG) or aerosol-OT (AOT), and the solubility, conformation, and catalytic activity of the modified subtilisins in some organic media were compared under the same conditions. The solubility of modified subtilisins depended on the solubility of the modifier. On the other hand, the conformational changes depended on the solubility, rather than the property, of the modifier. When the modified subtilisin was dissolved in water-miscible polar solvents such as dimethylsulfoxide, acetonitrile, and tetrahydrofuran, significant conformational changes occurred. When modified subtilisin was dissolved in water-immiscible organic solvents, such as isooctane and benzene, the solvent did not induce significant conformational changes. The catalytic activity in the transesterification reaction of the N-acetyl-L-phenylalanine ethylester of the modified subtilisin in organic solvents was higher than that of native subtilisin. The high activity of modified subtilisin was thought to be due to a homogeneous reaction by the dissolved enzymes.

Effect of pressure on the catalytic activity of subtilisin Carlsberg suspended in compressed gases

We studied the effect of pressure up to 300 bar on the catalytic efficiency of subtilisin Carlsberg suspended in compressed propane, near-critical ethane, near-critical carbon dioxide and tert-amyl alcohol, at constant temperature and fixed enzyme hydration. Increasing pressure lowered the catalytic efficiency of the enzyme in all the solvents, resulting in positive activation volumes, delta V#. The delta V# values in compressed propane and in tert-amyl alcohol were similar and larger in magnitude than the value reported in the literature for the same reaction in an aqueous buffer, although within the range of typical delta V# values in aqueous media. In the near-critical fluids, the delta V# were much larger, e.g., an increase in pressure of only 200 bar causing a sixfold decrease in the catalytic efficiency of subtilisin in carbon dioxide. These data should reflect the proximity of ethane and carbon dioxide to the critical point, and the resulting condensation of solvent molecules about the solutes, yielding negative solute partial molar volumes.