Structural and biochemical studies of GH family 12 cellulases: improved thermal stability, and ligand complexes

In this review we will describe how we have gathered structural and biochemical information from several homologous cellulases from one class of glycoside hydrolases (GH family 12), and used this information within the framework of a protein-engineering program for the design of new variants of these enzymes. These variants have been characterized to identify some of the positions and the types of mutations in the enzymes that are responsible for some of the biochemical differences in thermal stability and activity between the homologous enzymes. In this process we have solved the three-dimensional structure of four of these homologous GH 12 cellulases: Three fungal enzymes, Humicola grisea Cel12A, Hypocrea jecorina Cel12A and Hypocrea schweinitzii Cel12A, and one bacterial, Streptomyces sp. 11AG8 Cel12A. We have also determined the three-dimensional structures of the two most stable H. jecorina Cel12A variants. In addition, four ligand-complex structures of the wild-type H. grisea Cel12A enzyme have been solved and have made it possible to characterize some of the interactions between substrate and enzyme. The structural and biochemical studies of these related GH 12 enzymes, and their variants, have provided insight on how specific residues contribute to protein thermal stability and enzyme activity. This knowledge can serve as a structural toolbox for the design of Cel12A enzymes with specific properties and features suited to existing or new applications.     

Astaxanthin binding and structural stability of the apple snail carotenoprotein ovorubin

Ovorubin (OR) is the major perivitellin of the eggs of Pomacea canaliculata. The astaxanthin (ASX) binding and structural stability of OR were investigated by fluorescence spectroscopy and circular dichroism (CD). The apo-OR (without astaxanthin) shows a single, high affinity binding site for ASX (K(D)=0.5 microM). The quenching of tryptophan fluorescence by ASX indicates that about 22% are near the carotenoid-binding site in a non-polar environment, as indicated by tryptophan resonance energy transfer to the ligand. Secondary structure (alpha+beta) was virtually not affected by cofactor removal. Holo-OR shows unusually high thermal stability. The removal of ASX does not affect the thermal or chemical stability of the quaternary structure. In conclusion, although subtle changes were observed, ASX is not essential for OR stability, unlike most invertebrate carotenoproteins. This supports the idea that OR plays an important physiological role in the storage, transport and protection of carotenoids during snail embryogenesis.     

Effects of calcium binding on the structure and stability of human growth hormone

Thermodynamic analysis of calcium ions binding to human growth hormone (hGH) was done at 27 °C in NaCl solution, 50 mM, using different techniques. The binding isotherm for hGH-Ca²⁺ was obtained by two techniques of ionmetry, using a Ca²⁺-selective membrane electrode, and isothermal titration calorimetry. Results obtained by two ionmetric and calorimetric methods are in good agreement. There is a set of three identical and non-interacting binding sites for calcium ions. The intrinsic dissociation equilibrium constant and the molar enthalpy of binding are 52 μM and −17.4 kJ/mol, respectively. Temperature scanning UV–vis spectroscopy was applied to elucidate the effect of Ca²⁺ binding on the protein stability, and circular dichroism (CD) spectroscopy was used to show the structural change of hGH due to the metal ion interaction. Calcium ions binding increase the protein thermal stability by increasing of the alpha helix content as well as decreasing of both beta and random coil structures.     

结构指导的玉米赤霉烯酮水解酶的热稳定性改造

玉米赤霉烯酮是世界上污染最为广泛的一种镰刀菌(Fusarium)毒素,严重危害牲畜以及人类的健康。来源于粉红螺旋聚孢霉(Clonostachys rosea)的玉米赤霉烯酮水解酶(zearalenone hydrolase,ZHD)能有效降解饲料中的玉米赤霉烯酮,然而饲料加工中的高温环境限制了该酶的应用。基于结构特征的理性设计可为酶的热稳定性改造提供指导。本研究首先基于蛋白质结构比对(multiple structure alignment, MSTA)筛选ZHD的结构灵活区,随后基于序列保守性打分以及构象自由能计算设计突变文库,得到基于136号和220号残基的9个单点突变设计。结果表明,9个突变体的热熔融温度(Tm)提高了0.4–5.6℃,其中S220R和S220W热稳定性表现最好,Tm分别提高了5.6℃和4.0℃,45℃下的热半失活时间分别延长了15.4倍和3.1倍,相对酶活分别为野生型的70.6%和57.3%。分子动力学模拟分析表明突变位点及附近区域的作用力得到了增强,突变体S220R和S220W的220-K130氢键成键概率分别增加了37.1%和19.3%、K130-D223盐桥成键概率分别增加了30.1%和12.5%,为ZHD热稳定性的提高作出了贡献。这项工作表明结合天然酶的结构比对、序列分析及自由能计算的热稳定性改造策略的可行性,并获得了热稳定性增强的ZHD变体,为ZHD在工业上的应用打下基础。     

Opposing structural changes in two symmetrical polypeptides bring about opposing changes to the thermal stability of a complex integral membrane protein

The relationship between membrane protein structure and thermal stability has been examined in the reaction centre from the bacterium Rhodobacter sphaeroides, a complex membrane protein comprising three polypeptide chains and 10 cofactors. The core of this protein exhibits an approximate twofold symmetry, the cofactors being held in two membrane-spanning branches by two polypeptides, termed L and M, that have very similar folds. In assays of the thermal stability of wild-type and mutant reaction centres embedded in the native bilayer membrane, replacement of a Phe at position 197 of the M polypeptide by His produced an increase in stability, whereas an opposing replacement of His by Phe at the symmetrical position 168 of the L-polypeptide produced a decrease in stability. In light of the known X-ray crystal structures of wild-type and mutant variants of this protein, and further mutagenesis, it is concluded that these stability changes result from the introduction or removal, respectively, of a hydrogen bond between the side-chain of the His and that of an Asn located two positions along the M or L polypeptide chain, in addition to a hydrogen bond between the His side-chain and an adjacent bacteriochlorophyll cofactor.     

Metal-dependent thermal stability of recombinant endo-mannanase (ManB-1601) belonging to family GH 26 from Bacillus sp. CFR1601

A GH 26 endo-mannanase from Bacillus sp. CFR1601 was purified to homogeneity (M_w ∼39 kDa, specific activity 10,461.5 ± 100 IU/mg). Endo-mannanase gene (manb-1601, 1083 bp, accession No. KM404299) was expressed in Escherichia coli BL21 (DE3) and showed typical fingerprints of α/β proteins in the far-UV CD. A high degree of conservation among amino acid residues involved in metal chelation (His-1, 23 and Glu-336) and internal repeats (122–152 and 181–212) was observed in endo-mannanases reported from various Bacillus sp. Thermal inactivation kinetics suggested that metal ions are quintessential for stabilization of ManB-1601 structure as holoenzyme (E_a 87.4 kcal/mol, ΔH 86.7 kcal/mol, ΔS 186.6 cal/k/mol) displayed better values of thermodynamic parameters compared to metal-depleted ManB-1601 (E_a 47 kcal/mol, ΔH 45.7 kcal/mol, ΔS 64.7 cal/k/mol). EDTA treatment of ManB-1601 not only lead to transitions in both secondary and tertiary structure but also promulgated the population of conformational state that unfolds at lower temperature. ManB-1601 followed a three-state process for thermal inactivation wherein loss of tertiary structure preceded the concurrent loss of secondary structure and activity.     

木聚糖酶和甘露聚糖酶在毕赤酵母中的共表达及产酶分析

木聚糖酶和甘露聚糖酶是两种重要的半纤维素酶,也是两种重要的饲用酶制剂,通过毕赤酵母表达系统中的体外串联表达盒构建多拷贝的方法构建了木聚糖酶DSB和甘露聚糖酶Man A共表达重组质粒p PICZαA/DSB-ManA,将该重组质粒电转化至宿主菌毕赤酵母X33中获得共表达两种酶的重组菌X33/DSB-ManA,实现了两种酶的共分泌表达,经诱导表达后木聚糖酶和甘露聚糖酶的酶活分别为273. 6 U/ml和256. 8 U/ml,为单独表达重组菌X33/DSB和X33/Man A酶活的30. 4%和73. 4%。酶学性质的分析显示DSB和Man A的最适反应温度均为75℃,在45℃～75℃范围内具有较好的温度稳定性,酶活可保持最高酶活的60%以上; DSB最适pH为6. 5,Man A最适pH为6. 0,在pH 3. 0、40℃条件下,Man A处理1h能保持最高酶活的80%以上,DSB处理1 h时能保持最高酶活的50%以上; DSB和Man A对多种金属离子和化学试剂(浓度为1 mM)具有较好的耐受性,均可保留60%以上的酶活力。通过单一菌株成功完成了不同酶的共表达,为复合酶饲料添加剂的生产和应用研究提供了一定的理论依据。     

Role of weak interactions in thermal stability of proteins

A database analysis was done to study the role of weak interactions such as CHcdots, three dots, centeredO, CHcdots, three dots, centeredPI(m) and NHcdots, three dots, centeredPI(m) in the thermal stability of proteins. The CHcdots, three dots, centeredO and CHcdots, three dots, centeredPI(m) interactions are more in the case of thermophilic proteins as compared to mesophiles. Amino acid analysis showed that hydrophobic amino acids like Val and Ile, and Cys contribute more to CHcdots, three dots, centeredO hydrogen bonds where as Pro and Gly contribute more to CHcdots, three dots, centeredPI(m) interactions. Though NHcdots, three dots, centeredPI(m) interactions are dominated by Lys and Arg in thermophiles and mesophiles, the Arg contribution is significantly higher in thermophiles. Interestingly, Glycine is a predominant contributor to all the weak interactions. The number of aromatic amino acids in the thermophiles is more and hence a large number of aromatic clusters were observed in this class. Thus, a cumulative effect of weak interactions seems to be important in thermal stability of proteins. The study also shows that introduction of Gly, Arg, Phe, Pro, and Tyr may enhance the thermal stability.     

Effect of phosphorylation on the thermal and light stability of the thylakoid membranes

Higher plant thylakoid membranes contain a protein kinase that phosphorylates certain threonine residues of light-harvesting complex II (LHCII), the main light-harvesting antenna complexes of photosystem II (PSII) and some other phosphoproteins (Allen, Biochim Biophys Acta 1098:275, 1992). While it has been established that phosphorylation induces a conformational change of LHCII and also brings about changes in the lateral organization of the thylakoid membrane, it is not clear how phosphorylation affects the dynamic architecture of the thylakoid membranes. In order to contribute to the elucidation of this complex question, we have investigated the effect of duroquinol-induced phosphorylation on the membrane ultrastructure and the thermal and light stability of the chiral macrodomains and of the trimeric organization of LHCII. As shown by small angle neutron scattering on thylakoid membranes, duroquinol treatment induced a moderate (~10%) increase in the repeat distance of stroma membranes, and phosphorylation caused an additional loss of the scattering intensity, which is probably associated with the partial unstacking of the granum membranes. Circular dichroism (CD) measurements also revealed only minor changes in the chiral macro-organization of the complexes and in the oligomerization state of LHCII. However, temperature dependences of characteristic CD bands showed that phosphorylation significantly decreased the thermal stability of the chiral macrodomains in phosphorylated compared to the non-phosphorylated samples (in leaves and isolated thylakoid membranes, from 48.3°C to 42.6°C and from 47.5°C to 44.3°C, respectively). As shown by non-denaturing PAGE of thylakoid membranes and CD spectroscopy on EDTA washed membranes, phosphorylation decreased by about 5°C, the trimer-to-monomer transition temperature of LHCII. It also enhanced the light-induced disassembly of the chiral macrodomains and the monomerization of the LHCII trimers at 25°C. These data strongly suggest that phosphorylation of the membranes considerably facilitates the heat- and light-inducible reorganizations in the thylakoid membranes and thus enhances the structural flexibility of the membrane architecture.     

Synthesis, structural investigation and thermal stability of aqua magnesium(II) phthalocyanine adducts with 2-methoxyethylamine

Three new aqua magnesium phthalocyaninato complexes with 2-methoxyethylamine (MEA) in crystalline form have been obtained. The composition of the complexes depends on the crystallisation temperature. (MgPcH₂O)₂ · MEA (I) and (MgPcH₂O)₂ · 2MEA (II) were formed at about 170 °C and 80 °C, respectively, while room temperature (MgPcH₂O)₂ · 3MEA (III) was obtained. In all crystals the Mg atom is 4+1 coordinated, equatorially by four N-isoindole atoms of Pc ligand and axially by O atom of water molecule. The MgPc moiety is non-planar, the Mg(II) deviates by ∼0.5 Å from the N₄-isoindole plane towards the oxygen atom of water molecule. The MEA molecules in the crystals interact via hydrogen bonds with coordinated water molecules of MgPcH₂O. The arrangement of MgPcH₂O and 2-methoxyethylamine molecules is determined by O-H?N and O-H?O hydrogen bonds and by π-π interactions. The thermogravimetric analyses show characteristic steeps responsible for the loss of MEA molecules (at lower temperature) and water (at higher temperature) and finally all the complexes transform into β-MgPc. From among the complexes only complex II exhibits an intense near-IR absorption band in the solid-state, while spectra in MEA solution are identical for all the complexes.     

Comparison of family 12 glycoside hydrolases and recruited substitutions important for thermal stability

As part of a program to discover improved glycoside hydrolase family 12 (GH 12) endoglucanases, we have studied the biochemical diversity of several GH 12 homologs. The H. schweinitzii Cel12A enzyme differs from the T. reesei Cel12A enzyme by only 14 amino acids (93% sequence identity), but is much less thermally stable. The bacterial Cel12A enzyme from S. sp. 11AG8 shares only 28% sequence identity to the T. reesei enzyme, and is much more thermally stable. Each of the 14 sequence differences from H. schweinitzii Cel12A were introduced in T. reesei Cel12A to determine the effect of these amino acid substitutions on enzyme stability. Several of the T. reesei Cel12A variants were found to have increased stability, and the differences in apparent midpoint of thermal denaturation (T(m)) ranged from a 2.5 degrees C increase to a 4.0 degrees C decrease. The least stable recruitment from H. schweinitzii Cel12A was A35S. Consequently, the A35V substitution was recruited from the more stable S. sp. 11AG8 Cel12A and this T. reesei Cel12A variant was found to have a T(m) 7.7 degrees C higher than wild type. Thus, the buried residue at position 35 was shown to be of critical importance for thermal stability in this structural family. There was a ninefold range in the specific activities of the Cel12 homologs on o-NPC. The most and least stable T. reesei Cel12A variants, A35V and A35S, respectively, were fully active. Because of their thermal tolerance, S. sp. 11AG8 Cel12A and T. reesei Cel12A variant A35V showed a continual increase in activity over the temperature range of 25 degrees C to 60 degrees C, whereas the less stable enzymes T. reesei Cel12A wild type and the destabilized A35S variant, and H. schweinitzii Cel12A showed a decrease in activity at the highest temperatures. The crystal structures of the H. schweinitzii, S. sp. 11AG8, and T. reesei A35V Cel12A enzymes have been determined and compared with the wild-type T. reesei Cel12A enzyme. All of the structures have similar Calpha traces, but provide detailed insight into the nature of the stability differences. These results are an example of the power of homolog recruitment as a method for identifying residues important for stability.     

Respective importance of protein folding and glycosylation in the thermal stability of recombinant feruloyl esterase A

The thermal stability of four molecular forms (native, refolded, glycosylated, non-glycosylated) of feruloyl esterase A (FAEA) was studied. From the most to the least thermo-resistant, the four molecular species ranked as follows: (i) glycosylated form produced native, (ii) non-glycosylated form produced native, (iii) non-glycosylated form produced as inclusion bodies and refolded, and (iv) glycosylated form produced native chemically denatured and then refolded. On the basis of these results and of crystal structure data, we discuss the respective importance of protein folding and glycosylation in the thermal stability of recombinant FAEA.     

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8

The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.     

Enhancing the thermal stability of lipases through mutagenesis and immobilization on zeolites

The hydrolysis reaction of p-nitrophenyl butyrate catalyzed by lipases was followed with in situ UV/vis diode array spectrophotometry. Five enzymes - Candida antarctica lipase B and Fusarium solani pisi cutinase wild-type and three single-mutation variants - were tested as catalysts in homogeneous conditions and immobilized on zeolite NaY, on a polyacrylate support and as cross-linked aggregates. Using deconvolution techniques and kinetic modeling, the thermal stability of the different biocatalysts was compared in operational conditions and the results were supported by steady-state enzyme fluorescence measurements. We concluded that both the mutagenesis and the immobilization on zeolite NaY had a positive effect on the thermal stability of F. solani pisi cutinase.     

Enhancing effect of calcium and vanadium ions on thermal stability of bromoperoxidase from Corallina pilulifera

Bromoperoxidase from the macro-alga Corallina pilulifera is an enzyme that possesses vanadate in the catalytic center, and shows a significant thermostability and stability toward organic solvents. The structural analysis of the recombinant enzyme overexpressed in yeast revealed that it contains one calcium atom per subunit. This has been confirmed by inductively coupled plasma emission spectrometry experiments. The study of the effect of metal ions on the apo-enzyme stability has shown that the calcium ion significantly increased the enzyme stability. In addition, vanadate also increased the thermostability and strontium and magnesium ions had similar effects as calcium. The holo-enzyme shows high stability in a range of organic solvents. The effect of the different ions and solvents on the structure of the enzyme has been studied by circular dichroism experiments. The high stability of the enzyme in the presence of organic solvents is useful for its application as a biocatalyst.     

Role of calcium as trigger in thermal beta-lactoglobulin aggregation

Divalent calcium ions have been suggested to be involved in intermolecular protein-Ca2+-protein cross-linking, intramolecular electrostatic shielding, or ion-induced protein conformational changes as a trigger for protein aggregation at elevated temperatures. To address the first two phenomena in the case of beta-lactoglobulin, a combination of chemical protein modification, calcium-binding, and aggregation studies was used, while the structural integrity of the modified proteins was maintained. Although increasing the number of carboxylates on the protein by succinylation results in improved calcium-binding, calcium appears to be less effective in inducing protein aggregation. In fact, the larger the number of carboxylates, the higher the concentration of calcium that is required to trigger the aggregation. Lowering the number of negative charges on the protein surface via methylation of carboxylates reduces calcium-binding properties, but calcium-induced aggregation at low concentration is improved. Monovalent sodium ions cannot take over the specific role of calcium. The relation between net surface charge and number of calcium ions bound required to trigger the aggregation suggests that calcium needs to bind site specific to carboxylates with a threshold affinity. Subsequent site-specific screening of surface charges results in protein aggregation, driven by the partial unfolding of the protein at elevated temperatures, which is then facilitated by the absence of electrostatic repulsion.     

Factors affecting the stability of methanol dehydrogenase from Paracoccus denitrificans

Methanol dehydrogenase from Paracoccus denitrificans was purified to homogeneity in two steps from the periplasmic fraction of methanol-grown cells. The enzyme was composed of subunits of M(r) 67,000 and 12,000, and non-covalently bound pyrroloquinoline quinone. It exhibited a pH optimum at pH values of 9.0 and above. It was not stable at pH greater than 9.0, but exhibited little loss of activity after prolonged incubation at pH values as low as 4.5. Methyl dehydrogenase was relatively stable to thermal denaturation. The thermal stability was enhanced by the presence of Ca2+ and diminished by the presence of EDTA. These data suggest a structural role for Ca2+ in this enzyme, similar to what has been observed with quinoprotein glucose and ethanol dehydrogenases.     

Effects of calcium on the thermal stability, stability in organic solvents and resistance to hydrogen peroxide of artichoke (Cynara scolymus L.) peroxidase: A potential method of enzyme control

The effects of calcium ions (Ca²⁺) on the stability of artichoke (Cynara scolymus L.) peroxidase (AKPC) have been studied. The thermal stability of AKPC was improved by the addition of Ca²⁺; the melting temperature increased by 20 °C and the deactivation energy by 26 kJ mol⁻¹. AKPC was stable in a selection of organic solvents but was less active with 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) than under aqueous conditions. Ca²⁺-free AKPC retained more activity in the presence of organic solvents due to its better maintenance of the rate of compound I formation with hydrogen peroxide (H₂O₂) compared to AKPC-Ca²⁺. AKPC retained at least 75% activity over 24 h in the pH range 3.0–10.5 and about 50% over 1 month at pH 7.0 or 5.5, irrespective of the Ca²⁺ content. AKPC-Ca²⁺ was considerably more resistant to inactivation by H₂O₂ than Ca²⁺-free AKPC suggesting that the presence of Ca²⁺ boosts turnover under oxidizing conditions. AKPC has been applied as an alternative to horseradish peroxidase (HRP) in glucose concentration assays; the presence of Ca²⁺ or of the Ca²⁺ chelating agent ethylenediaminetetraacetic acid made no difference to the final result. The possibility is discussed that addition and removal of a labile Ca²⁺ from AKPC could be used to control enzyme activity both in vivo and in vitro.