Rational Enzyme Design Research Articles

Structural insights into the binding and catalytic mechanisms of the Listeria monocytogenes bacteriophage glycosyl hydrolase PlyP40.

Endolysins are bacteriophage-encoded peptidoglycan hydrolases that specifically degrade the bacterial cell wall at the end of the phage lytic cycle. They feature a distinct modular architecture, consisting of enzymatically active domains (EADs) and cell wall-binding domains (CBDs). Structural analysis of the complete enzymes or individual domains is required for better understanding the mechanisms of peptidoglycan degradation and provides guidelines for the rational design of chimeric enzymes. We here report the crystal structure of the EAD of PlyP40, a member of the GH-25 family of glycosyl hydrolases, and thefirst muramidase reported for Listeria phages. Site-directed mutagenesis confirmed key amino acids (Glu98 and Trp10) involved in catalysis and substrate stabilization. In addition, we found that PlyP40 contains two heterogeneous CBD modules with homology to SH3 and LysM domains. Truncation analysis revealed that both domains are required for full activity but contribute to cell wall recognition and lysis differently. Replacement of CBDP40 with a corresponding domain from a different Listeria phage endolysin yielded an enzyme with a significant shift in pH optimum. Finally, domain swapping between PlyP40 and the streptococcal endolysin Cpl-1 produced an intergeneric chimera with activity against Listeria cells, indicating that structural similarity of individual domains determines enzyme function.

Catalytic Function and Application of Cytochrome P450 Enzymes in Biosynthesis and Organic Synthesis

Cytochrome P450 enzymes are widely distributed in nature, which mainly participate in xenobiotics metabolism and natural product biosynthesis. These enzymes are able to recognize various substrates to produce many useful oxidative products through diverse reaction types. P450 enzymes can catalyze selective oxidation of C-H bonds in their substrates under mild conditions. Therefore, a lot of P450 enzymes have been applied in the production of fine chemicals, drugs and chemical intermediates for quite a long time. With the development of protein engineering, redox partner engineering, substrate engineering, metabolic engineering and synthetic biology, it has become possible to obtain the P450 biocatalysts with the desired properties such as high activity, the substrate specificity of interest, and great selectivity to meet the industrial requirements, through rational design and direct evolution of P450 enzymes. Thus, the application scope of P450 enzymes in biosynthesis and organic synthesis has been expanded greatly. The types of reactions that can be catalyzed by P450 enzymes, and the strategies to broaden the reaction scope and to enhance the catalytic efficiency and selectivity are summarized. Finally, the challenges and prospects in the application of cytochrome P450 enzymes in biosynthesis and organic synthesis are discussed.

Molecular dynamics derived life times of active substrate binding poses explain K M of laccase mutants.

Fungal laccases (EC 1.10.3.2) are important multi-copper oxidases with broad substrate specificity. Laccases from Trametes versicolor (TvL) are among the best-characterized of these enzymes. Mutations in the substrate-binding site of TvL substantially affect KM, but a molecular understanding of this effect is missing. We explored the effect of TvL mutations on KM for the standard laccase substrate 2,6-dimethoxyphenol using 4500 ns of molecular dynamics, docking, and MMGBSA free energy computations. We show that changes in KM due to mutation consistently correlate with the dynamics of the substrates within the substrate-binding site. We find that KM depends on the lifetime (“dynamic stability”) of the enzyme-substrate complex as commonly assumed. We then further show that MMGBSA-derived free energies of substrate binding in the active pose consistently reproduce large vs. small experimental KM values. Our results indicate that hydrophobic packing of the substrate near the T1 binding site of the laccase is instrumental for high turnover via KM. We also address the more general question of how enzymes such as laccases gain advantage of lower KM despite the Sabatier principle, which disfavors a stable enzyme–substrate complex. Our data suggest that the observed KM relates directly to the lifetime of the active substrate pose within a protein. In contrast, the thermochemical stability of the enzyme–substrate complex reflects an ensemble average of all enzyme–substrate binding poses. This distinction may explain how enzymes work by favoring longer residence time in the active pose without too favorable general enzyme–substrate interactions, a principle that may aid the rational design of enzymes.

Molecular insights into the role of a distal F240A mutation that alters CYP1A1 activity towards persistent organic pollutants

BackgroundCytochromes P450 are major drug-metabolizing enzymes involved in the biotransformation of diverse xenobiotics and endogenous chemicals. Persistent organic pollutants (POPs) are toxic hydrophobic compounds that cause serious environmental problems because of their poor degradability. This calls for rational design of enzymes capable of catalyzing their biotransformation. Cytochrome P450 1A1 isoforms catalyze the biotransformation of some POPs, and constitute good starting points for the design of biocatalysts with tailored substrate specificity. MethodsWe rationalized the activities of wild type and mutant forms of rat cytochrome P450 1A1 towards 2,3,7,8-tetrachloro-dibenzo-p-dioxin (TCDD) and 3,3′,4,4′-tetrachlorobiphenyl (PCB77) using experiments and molecular dynamics simulations. ResultsWe showed that the enhanced activity of the CYP1A1 mutant towards TCDD was due to more efficient binding of the substrate in the active site even though the mutated site was over 2.5nm away from the catalytic center. Moreover, this mutation reduced activity towards PCB77. General significanceAmino acids that affect substrate access channels can be viable targets for rational enzyme design even if they are located far from the catalytic site.

Computational study of the binding mechanism of medium chain acyl-CoA synthetase with substrate in Methanosarcina acetivorans

The acyl-AMP forming family of adenylating enzymes catalyzes the formation of acyl-CoA from an acyl substrate, ATP, and CoA, which is a metabolite of many catabolic and anabolic processes. The medium-chain acyl-CoA synthetase from Methanosarcina acetivorans, designated MacsMa, uses 2-methylbutyrate as its preferred substrate. It is reported that the interaction between the sidechain of Cys298 and Lys256 of this enzyme is important for the catalytic activity. The mutation of these residues resulted in the changes of the structure stability and the reduced or absence catalytic activity. In the present study, the binding mechanism between the substrate 2-methylbutyrate- AMP (2MeBA) and MacsMa were explored by integrating multiple computational methods including molecular docking, molecular dynamics simulations, binding free energy calculation, active site access channel analysis and principal component analysis. The binding free energy between WT, mutated Macs and substrate was calculated by MM-GBSA method, which indicated that the binding affinity between this enzyme and substrate was stronger in the WT than that in the mutated forms (K256L, K256T and C298Y). Per-residue binding free energy decomposition identified some residues, such as Gly327, Phe350, Gly351, Gln352 and Lys461, which are important for the enzyme and substrate binding affinity. The access channels of the mutant system (MacsK256L, MacsK256T and MacsC298Y) were found to be different from those in the wild-type systems. It suggested that K256L and C298Y induced larger flexibility to the overall protein compared with the WT, whereas K256T induced larger flexibility to the partial protein compared with the WT by PCA vector porcupines. This study provides novel insight to understand the substrate binding mechanism of Macs and useful information for the rational enzyme design.

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium.

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs shows that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. These results are directly applicable to rational enzyme design and engineering.

Revealing the Roles of Subdomains in the Catalytic Behavior of Lipases/Acyltransferases Homologous to CpLIP2 through Rational Design of Chimeric Enzymes.

The lipases/acyltransferases homologous to CpLIP2 of Candida parapsilosis efficiently catalyze acyltransfer reactions in lipid/water media with high water activity (aW >0.9). Two new enzymes of this family, CduLAc from Candida dubliniensis and CalLAc8 from Candida albicans, were characterized. Despite 82 % sequence identity, the two enzymes have significant differences in their catalytic behaviors. In order to understand the roles played by the different subdomains of these proteins (main core, cap and C-terminal flap), chimeric enzymes were designed by rational exchange of cap and C-terminal flap, between CduLAc and CalLAc8. The results show that the cap region plays a significant role in substrate specificity; the main core was found to be the most important part of the protein for acyltransfer ability. Similar exchanges were made with CAL-A from Candida antarctica, but only the C-terminal exchange was successful. Yet, the role of this domain was not clearly elucidated, other than that it is essential for activity.

Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways.

Cytochrome P450 OleTJE has attracted much attention for its ability to catalyze the decarboxylation of long chain fatty acids to generate alkenes, which are not only biofuel molecule, but also can be used broadly for making lubricants, polymers and detergents. In this study, the molecular basis of the binding mechanism of P450 OleTJE for arachidic acid, myristic acid, and caprylic acid was investigated by utilizing conventional molecular dynamics simulation and binding free energy calculations. Moreover, random acceleration molecular dynamics (RAMD) simulations were performed to uncover the most probable access/egress channels for different fatty acids. The predicted binding free energy shows an order of arachidic acid < myristic acid < caprylic acid. Key residues interacting with three substrates and residues specifically binding to one of them were identified. The RAMD results suggest the most likely channel for arachidic acid, myristic acid, and caprylic acid are 2e/2b, 2a and 2f/2a, respectively. It is suggested that the reaction is easier to carry out in myristic acid bound system than those in arachidic acid and caprylic acid bound system based on the distance of Hβ atom of substrate relative to P450 OleTJE Compound I states. This study provided novel insight to understand the substrate preference mechanism of P450 OleTJE and valuable information for rational enzyme design for short chain fatty acid decarboxylation.

Nano-Armoring of Enzymes: Rational Design of Polymer-Wrapped Enzymes.

The formulation in which therapeutic proteins are administered plays a key role in retaining their biological activity. Enzyme wrapping, using synthetic polymers, is a strategy employed to provide enzymes with lower immunogenicity, longer circulation times, and better targeting capabilities. Protein-polymer complexation methods, involving covalent, noncovalent, and electrostatic interactions, that can provide means to develop formulations for retaining enzyme stability are discussed in this chapter. Amphiphilic self-cross-linkable polymer was used to encapsulate capsase-3 enzyme in the nanogel, while inverse emulsion polymerization method was used to entrap α-glucosidase enzyme in the nanogel. These nanogels were characterized by dynamic light scattering, transmission electron microscopy, and gel electrophoresis. Upon release of caspase-3 enzyme from polymeric nanogel, it retained nearly 86% of its original activity. Similarly, α-glucosidase that was encased in the acid cleavable polymeric nanogel exhibited substantial activity after release under acidic conditions (pH 5, 48h). Nano-armoring of the enzymes were nearly complete and provided high yields of the encased enzyme.

Identification of bean hydroxycinnamoyl-CoA:tetrahydroxyhexanedioate hydroxycinnamoyl transferase (HHHT): use of transgenic alfalfa to determine acceptor substrate specificity.

Transgenic alfalfa ( Medicago sativa L.) provides a useful reverse genetics platform to elucidate acceptor substrate specificity for uncharacterized BAHD family hydroxycinnamoyl-CoA hydroxycinnamoyl transferases. Tissues of many plant species accumulate hydroxycinnamoyl derivatives, often esters, thought to serve in protection against biotic and abiotic stresses. In many cases, these specialized metabolites are produced by BAHD family hydroxycinnamoyl-CoA hydroxycinnamoyl transferases (HCTs). Bean (Phaseolus vulgaris) leaves contain both hydroxycinnamoyl-malate esters and an HCT activity capable of making them. In seeking to identify this HCT from bean, we identified a gene whose predicted protein showed a high degree of sequence similarity (75%) to the Trifolium pratense (red clover) enzyme that carries out this reaction. The encoded bean protein, however, failed to carry out the malate transfer reaction when expressed in Escherichia coli. Expression of the gene in alfalfa (Medicago sativa) resulted in accumulation of several new hydroxycinnamates not present in nontransformed alfalfa, many of which corresponded to phenolics present in bean. Using accurate mass and UV absorption spectral data, we identified the acceptor substrate for this HCT as tetrahydroxyhexanedioic acids and demonstrated this predicted transferase activity with the E. coli-expressed protein. This finding adds to the growing number of BAHD family HCTs that have been characterized with respect to substrate specificity. Such data, combined with primary sequence and protein structural data will allow for a better understanding of the structure/function relationships of these enzymes and may eventually aid the rational design of such enzymes for altered substrate specificities. Additionally, expression of HCTs of unknown substrate specificity in alfalfa and characterization of the resulting accumulated novel metabolites could be a useful approach to characterizing putative BAHD HCT enzymes.

Investigation of structural stability and enzymatic activity of glucose oxidase and its subunits

Glucose oxidase (β-d-glucose:oxygen 1-oxidoreductase, EC 1.1.3.4) catalyzes the oxidation of β-d glucose utilizing molecular oxygen as an electron acceptor to produce d-glucono-1,5-lactoneand hydrogen peroxide, which has applications in food, biotechnology and medical industries. It was known that dimer form was considered to be active and monomer form has inactive conformation. However, there are no evidences at the molecular levels for Glucose oxidase (GOx) inactivation through dissociation. Here, using molecular dynamic simulation, it has been investigated for the first time that why dimer form of the enzyme is active. We have performed a series of molecular dynamics simulations at different forms of GOx (monomer and dimer with and without FAD cofactor). The analysis of tertiary structure showed that monomer is more unstable and has more deviation from the crystal structure. In contrast, dimer has a stable conformation during simulation. These results are in good agreement with experimental data about enzyme inactivation by dissociation. It was also found that when FAD is removed from monomer, it became more unstable in comparison with monomer containing cofactor. This shows essential role of FAD in both activity and stability of the enzyme. According to the MD simulation, enzyme inactivation is associated with changing in secondary structure at the interface. Interestingly, it was found that some secondary structures are destructed while some structures are formed in monomer upon dissociation. The analysis of active site structure during simulation revealed that both dissociation and release of the FAD influence on inactivation of GOx. This study provided novel insight to understand the mechanism of enzyme inactivation upon dissociation, which would be useful for rational enzyme design.

Rate of Threading a Cellulose Chain into the Binding Tunnel of a Cellulase.

Industrially important cellulase Cel7A hydrolyzes crystalline cellulose by a complex processive mechanism in which the enzyme slides along the cellulose surface with one strand of the polymeric substrate channeled through its catalytic tunnel. Each processive run must start with threading the tunnel with a cellulose strand and end with the opposite, that is, the dethreading process. Evidence has suggested that threading or dethreading may be rate-limiting for the overall enzyme reaction. To directly elucidate the rates of threading and dethreading, we analyzed experimental data with respect to a two-step model that distinguishes enzymes in free, associated nonthreaded, and threaded states. This approach enabled the estimation of rate constants for both steps in both directions. The results showed that Cel7A utilizes a "tapping" mode of attack, in which it associates unproductively with the cellulose surface many times before it eventually finds a location at which it gets threaded. Moreover, it was concluded that at the quasi steady state dethreading was the main determinant of the overall hydrolytic rate under most conditions. An exception to this was at very low enzyme/substrate ratios, at which other steps also influenced the overall dynamics. These results will be helpful in identifying rate-limiting steps for cellulases and, in turn, targets for rational design of faster enzymes.

Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis.

Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.

Mechanisms of Oxidase and Superoxide Dismutation-like Activities of Gold, Silver, Platinum, and Palladium, and Their Alloys: A General Way to the Activation of Molecular Oxygen.

Metal and alloy nanomaterials have intriguing oxidase- and superoxide dismutation-like (SOD-like) activities. However, origins of these activities remain to be studied. Using density functional theory (DFT) calculations, we investigate mechanisms of oxidase- and SOD-like properties for metals Au, Ag, Pd and Pt and alloys Au4-xMx (x = 1, 2, 3; M = Ag, Pd, Pt). We find that the simple reaction-dissociation of O2-supported on metal surfaces can profoundly account for the oxidase-like activities of the metals. The activation (Eact) and reaction energies (Er) calculated by DFT can be used to effectively predict the activity. As verification, the calculated activity orders for series of metal and alloy nanomaterials are in excellent agreement with those obtained by experiments. Briefly, the activity is critically dependent on two factors, metal compositions and exposed facets. On the basis of these results, an energy-based model is proposed to account for the activation of molecular oxygen. As for SOD-like activities, the mechanisms mainly consist of protonation of O2(•-) and adsorption and rearrangement of HO2(•) on metal surfaces. Our results provide atomistic-level insights into the oxidase- and SOD-like activities of metals and pave a way to the rational design of mimetic enzymes based on metal nanomaterials. Especially, the O2 dissociative adsorption mechanism will serve as a general way to the activation of molecular oxygen by nanosurfaces and help understand the catalytic role of nanomaterials as pro-oxidants and antioxidants.

Structural basis for catalytically restrictive dynamics of a high-energy enzyme state.

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or ‘invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power—a key aspect in rational design of enzymes catalysing novel reactions.

Improving thermal and detergent stability of Bacillus stearothermophilus neopullulanase by rational enzyme design.

Neopullulanase, a glycosyl hydrolase from Bacillus stearothermophilus (bsNpl), is a potentially valuable enzyme for starch and detergent industries. However, as the protein is not active at elevated temperatures and high surfactant concentrations, we aimed to increase its stability by rational enzyme design. Nine potentially destabilizing cavities were identified in the crystal structure of the enzyme. Based on computational predictions, these cavities were filled by residues with bulkier side chains. The five Asp46Glu, Val239Leu, Val404Leu, Ser407Thr and Ala566Leu exchanges resulted in a drastic stabilization of bsNpl against inactivation by heat and detergents. The catalytic activity of the variants was identical to the wild-type enzyme.

Kinetics of Cellobiohydrolase (Cel7A) Variants with Lowered Substrate Affinity

Cellobiohydrolases are exo-active glycosyl hydrolases that processively convert cellulose to soluble sugars, typically cellobiose. They effectively break down crystalline cellulose and make up a major component in industrial enzyme mixtures used for deconstruction of lignocellulosic biomass. Identification of the rate-limiting step for cellobiohydrolases remains controversial, and recent reports have alternately suggested either association (on-rate) or dissociation (off-rate) as the overall bottleneck. Obviously, this uncertainty hampers both fundamental mechanistic understanding and rational design of enzymes with improved industrial applicability. To elucidate the role of on- and off-rates, respectively, on the overall kinetics, we have expressed a variant in which a tryptophan residue (Trp-38) in the middle of the active tunnel has been replaced with an alanine. This mutation weakens complex formation, and the population of substrate-bound W38A was only about half of the wild type. Nevertheless, the maximal, steady-state rate was twice as high for the variant enzyme. It is argued that these opposite effects on binding and activity can be reconciled if the rate-limiting step is after the catalysis (i.e. in the dissociation process).

Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates

Optically pure epoxides are essential chiral precursors for the production of (S)-propranolol, (S)-alprenolol, and other β-adrenergic receptor blocking drugs. Although the enzymatic production of these bulky epoxides has proven difficult, here we report a method to effectively improve the activity of BmEH, an epoxide hydrolase from Bacillus megaterium ECU1001 toward α-naphthyl glycidyl ether, the precursor of (S)-propranolol, by eliminating the steric hindrance near the potential product-release site. Using X-ray crystallography, mass spectrum, and molecular dynamics calculations, we have identified an active tunnel for substrate access and product release of this enzyme. The crystal structures revealed that there is an independent product-release site in BmEH that was not included in other reported epoxide hydrolase structures. By alanine scanning, two mutants, F128A and M145A, targeted to expand the potential product-release site displayed 42 and 25 times higher activities toward α-naphthyl glycidyl ether than the wild-type enzyme, respectively. These results show great promise for structure-based rational design in improving the catalytic efficiency of industrial enzymes for bulky substrates.

Computational Mutation Design of Diol Dehydratase: Catalytic Ability toward Glycerol beyond the Wild-Type Enzyme

Abstract A computational mutation analysis based on quantum mechanical/molecular mechanical (QM/MM) calculations is performed for the elucidation of catalytic functions of amino acid residues at the active site of diol dehydratase in the dehydration of glycerol to afford 3-hydroxypropionaldehyde. While the wild-type diol dehydratase is subject to suicide inactivation in the dehydration process, mutants Gln336Ala and Ser301Ala are more resistant to the inactivation by glycerol (Yamanishi et al., FEBS J.2012, 279, 793). In the present study the impact of the mutation is discussed on the basis of energy profiles of two reaction pathways for the dehydration of glycerol and the inactivation of the enzyme. Both the mutants efficiently distinguish between two possible binding conformations of glycerol, the GS and GR conformations, where the former is known to mainly contribute to the inactivation of the enzyme. The improved resistance to the inactivation observed for the mutants can be explained by a hydrogen-bonding interaction between an OH group of glycerol and Ser301 as well as steric repulsion between glycerol and Val300. The computational mutation analysis first unveils the vital role of Val300 in the discrimination of the GS and GR conformations, which was not clearly viewed in the wild-type enzyme. The present findings will encourage the application of computational mutation approach to the rational design of enzymes optimized for desired organic synthesis.

Engineering acidic Streptomyces rubiginosus D-xylose isomerase by rational enzyme design

To maximize bioethanol production from lignocellulosic biomass, all sugars must be utilized. Yeast fermentation can be improved by introducing the d-xylose isomerase enzyme to convert the pentose sugar d-xylose, which cannot be fermented by Saccharomyces cerevisiae, into the fermentable ketose d-xylulose. The low activity of d-xylose isomerase, especially at the low pH required for optimal fermentation, limits its use. A rational enzyme engineering approach was undertaken, and seven amino acid positions were replaced to improve the activity of Streptomyces rubiginosus d-xylose isomerase towards its physiological substrate at pH values below 6. The active-site design was guided by mechanistic insights and the knowledge of amino acid protonation states at low pH obtained from previous joint X-ray/neutron crystallographic experiments. Tagging the enzyme with 6 or 12 histidine residues at the N-terminus resulted in a significant increase in the active-site affinity towards substrate at pH 5.8. Substituting an asparagine at position 215, which hydrogen bonded to the metal-bound Glu181 and Asp245, with an aspartate gave a variant with almost an order of magnitude lower KM than measured for the native enzyme, with a 4-fold increase in activity. Other studied variants showed similar (Asp57Asn, Glu186Gln/Asn215Asp), lower (Asp57His, Asn247Asp, Lys289His, Lys289Glu) or no (Gln256Asp, Asp287Asn, ΔAsp287) activity in acidic conditions relative to the native enzyme.