Entropies of redox reactions between proteins and mediators: the temperature dependence of reversible electrode potentials in aqueous buffers

Functional characterization of a lytic polysaccharide monooxygenase from Schizophyllum commune that degrades non-crystalline substrates

Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that use O2 or H2O2 to oxidatively cleave glycosidic bonds. LPMOs are prevalent in nature, and the functional variation among these enzymes is a topic of great interest. We present the functional characterization of one of the 22 putative AA9-type LPMOs from the fungus Schizophyllum commune, ScLPMO9A. The enzyme, expressed in Escherichia coli, showed C4-oxidative cleavage of amorphous cellulose and soluble cello-oligosaccharides. Activity on xyloglucan, mixed-linkage β-glucan, and glucomannan was also observed, and product profiles differed compared to the well-studied C4-oxidizing NcLPMO9C from Neurospora crassa. While NcLPMO9C is also active on more crystalline forms of cellulose, ScLPMO9A is not. Differences between the two enzymes were also revealed by nuclear magnetic resonance (NMR) titration studies showing that, in contrast to NcLPMO9C, ScLPMO9A has higher affinity for linear substrates compared to branched substrates. Studies of H2O2-fueled degradation of amorphous cellulose showed that ScLPMO9A catalyzes a fast and specific peroxygenase reaction that is at least two orders of magnitude faster than the apparent monooxygenase reaction. Together, these results show that ScLPMO9A is an efficient LPMO with a broad substrate range, which, rather than acting on cellulose, has evolved to act on amorphous and soluble glucans.

Initial characterization of an iron superoxide dismutase from Thermobifida fusca

Superoxide dismutases (SODs) are enzymes that catalyze the dismutation of the superoxide radical anion into O2 and H2O2 in a two-step reaction. They are ubiquitous to all forms of life and four different types of metal centers are detected, dividing this class of enzymes into Cu-/Zn-, Ni-, Mn-, and Fe-SODs. In this study, a superoxide dismutase from the thermophilic bacteria Thermobifida fusca (TfSOD) was cloned and expressed before the recombinant enzyme was characterized. The enzyme was found to be active for superoxide dismutation measured by inhibition of cytochrome c oxidation and the inhibition of the autoxidation of pyrogallol. Its pH-optimum was determined to be 7.5, while it has a broad temperature optimum ranging from 20 to 90 °C. Combined with the Tm that was found to be 78.5 ± 0.5 °C at pH 8.0, TfSOD can be defined as a thermostable enzyme. Moreover, the crystal structure of TfSOD was determined and refined to 1.25 Å resolution. With electron paramagnetic resonance spectroscopy, it was confirmed that iron is the metal co-factor of TfSOD. The cell potential (Em) for the TfSOD-Fe3+/TfSOD-Fe2+ redox couple was determined to be 287 mV.

Structural and functional characterization of the catalytic domain of a cell-wall anchored bacterial lytic polysaccharide monooxygenase from Streptomyces coelicolor

Bacterial lytic polysaccharide monooxygenases (LPMOs) are known to oxidize the most abundant and recalcitrant polymers in Nature, namely cellulose and chitin. The genome of the model actinomycete Streptomyces coelicolor A3(2) encodes seven putative LPMOs, of which, upon phylogenetic analysis, four group with typical chitin-oxidizing LPMOs, two with typical cellulose-active LPMOs, and one which stands out by being part of a subclade of non-characterized enzymes. The latter enzyme, called ScLPMO10D, and most of the enzymes found in this subclade are unique, not only because of variation in the catalytic domain, but also as their C-terminus contains a cell wall sorting signal (CWSS), which flags the LPMO for covalent anchoring to the cell wall. Here, we have produced a truncated version of ScLPMO10D without the CWSS and determined its crystal structure, EPR spectrum, and various functional properties. While showing several structural and functional features typical for bacterial cellulose active LPMOs, ScLPMO10D is only active on chitin. Comparison with two known chitin-oxidizing LPMOs of different taxa revealed interesting functional differences related to copper reactivity. This study contributes to our understanding of the biological roles of LPMOs and provides a foundation for structural and functional comparison of phylogenetically distant LPMOs with similar substrate specificities.

Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens

The monoheme outer membrane cytochrome F (OmcF) from Geobacter sulfurreducens plays an important role in Fe(III) reduction and electric current production. The electrochemical characterization of this cytochrome has shown that its redox potential is modulated by the solution pH (redox-Bohr effect) endowing the protein with the necessary properties to couple electron and proton transfer in the physiological range. The analysis of the OmcF structures in the reduced and oxidized states showed that with the exception of the side chain of histidine 47 (His⁴⁷), all other residues with protonatable side chains are distant from the heme iron and, therefore, are unlikely to affect the redox potential of the protein. The protonatable site at the imidazole ring of His⁴⁷ is in the close proximity to the heme and, therefore, this residue was suggested as the redox-Bohr center. In the present work, we tested this hypothesis by replacing the His⁴⁷ with non-protonatable residues (isoleucine – OmcFH47I and phenylalanine – OmcFH47F). The structure of the mutant OmcFH47I was determined by X-ray crystallography to 1.13 Å resolution and showed only minimal changes at the site of the mutation. Both mutants were ¹⁵N-labeled and their overall folding was confirmed to be the same as the wild-type by NMR spectroscopy. The pH dependence of the redox potential of the mutants was measured by cyclic voltammetry. Compared to the wild-type protein, the magnitude of the redox-Bohr effect in the mutants was smaller, but not fully abolished, confirming the role of His⁴⁷ on the pH modulation of OmcF’s redox potential. However, the pH effect on the heme substituents’ NMR chemical shifts suggested that the heme propionate P₁₃ also contributes to the overall redox-Bohr effect in OmcF. In physiological terms, the contribution of two independent acid–base centers to the observed redox-Bohr effect confers OmcF a higher versatility to environmental changes by coupling electron/proton transfer within a wider pH range.

Methylation of the N-terminal histidine protects a lytic polysaccharide monooxygenase from auto-oxidative inactivation

The catalytically crucial N-terminal histidine (His1) of fungal lytic polysaccharide monooxygenases (LPMOs) is post-translationally modified to carry a methylation. The functional role of this methylation remains unknown. We have carried out an in-depth functional comparison of two variants of a family AA9 LPMO from Thermoascus aurantiacus (TaLPMO9A), one with, and one without the methylation on His1. Various activity assays showed that the two enzyme variants are identical in terms of substrate preferences, cleavage specificities and the ability to activate molecular oxygen. During the course of this work, new functional features of TaLPMO9A were discovered, in particular the ability to cleave xyloglucan, and these features were identical for both variants. Using a variety of techniques, we further found that methylation has minimal effects on the pK_a of His1, the affinity for copper and the redox potential of bound copper. The two LPMOs did, however, show clear differences in their resistance against oxidative damage. Studies with added hydrogen peroxide confirmed recent claims that low concentrations of H₂ O₂ boost LPMO activity, whereas excess H₂ O₂ leads to LPMO inactivation. The methylated variant of TaLPMO9A, produced in Aspergillus oryzae, was more resistant to excess H₂ O₂ and showed better process performance when using conditions that promote generation of reactive-oxygen species. LPMOs need to protect themselves from reactive oxygen species generated in their active sites and this study shows that methylation of the fully conserved N-terminal histidine provides such protection.

Thermodynamic and kinetic properties of the outer membrane cytochrome OmcF, a key protein for extracellular electron transfer in Geobacter sulfurreducens

Gene knock-out studies on Geobacter sulfurreducens have shown that the monoheme c-type cytochrome OmcF is essential for the extracellular electron transfer pathways involved in the reduction of iron and uranium oxy-hydroxides, as well as, on electricity production in microbial fuel cells. A detailed electrochemical characterization of OmcF was performed for the first time, allowing attaining kinetics and thermodynamic data. The heterogeneous electron transfer rate constant was determined at pH 7 (0.16 ± 0.01 cm s^-1) indicating that the protein displays high electron transfer efficiency compared to other monoheme cytochromes. The pH dependence of the redox potential indicates that the protein has an important redox-Bohr effect in the physiological pH range for G. sulfurreducens growth. The analysis of the structures of OmcF allowed us to assign the redox-Bohr centre to the side chain of His⁴⁷ residue and its pK_a values in the reduced and oxidized states were determined (pK_ox = 6.73; pK_red = 7.55). The enthalpy, entropy and Gibbs free energy associated with the redox transaction were calculated, pointing the reduced form of the cytochrome as the most favourable. The data obtained indicate that G. sulfurreducens cells evolved to warrant a down-hill electron transfer from the periplasm to the outer-membrane associated cytochrome OmcF.

Analytical Tools for Characterizing Cellulose-Active Lytic Polysaccharide Monooxygenases (LPMOs)

Lytic polysaccharide monooxygenases are copper-dependent enzymes that perform oxidative cleavage of glycosidic bonds in cellulose and various other polysaccharides. LPMOs acting on cellulose use a reactive oxygen species to abstract a hydrogen from the C1 or C4, followed by hydroxylation of the resulting substrate radical. The resulting hydroxylated species is unstable, resulting in glycoside bond scission and formation of an oxidized new chain end. These oxidized chain ends are spontaneously hydrated at neutral pH, leading to formation of an aldonic acid or a gemdiol, respectively. LPMO activity may be characterized using a variety of analytic tools, the most common of which are high-performance anion exchange chromatography system with pulsed amperometric detection (HPAEC-PAD) and MALDI-TOF mass spectrometry (MALDI-MS). NMR may be used to increase the certainty of product identifications, in particular the site of oxidation. Kinetic studies of LPMOs have several pitfalls and to avoid these, it is important to secure copper saturation, avoid the presence of free transition metals in solution, and control the amount of reductant (i.e., electron supply to the LPMO). Further insight into LPMO properties may be obtained by determining the redox potential and by determining the affinity for copper. In some cases, substrate affinity can be assessed using isothermal titration calorimetry. These methods are described in this chapter.

Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity

The recently discovered lytic polysaccharide monooxygenases (LPMOs) carry out oxidative cleavage of polysaccharides and are of major importance for efficient processing of biomass. NcLPMO9C from Neurospora crassa acts both on cellulose and on non-cellulose β-glucans, including cellodextrins and xyloglucan. The crystal structure of the catalytic domain of NcLPMO9C revealed an extended, highly polar substrate-binding surface well suited to interact with a variety of sugar substrates. The ability of NcLPMO9C to act on soluble substrates was exploited to study enzyme-substrate interactions. EPR studies demonstrated that the Cu(2+) center environment is altered upon substrate binding, whereas isothermal titration calorimetry studies revealed binding affinities in the low micromolar range for polymeric substrates that are due in part to the presence of a carbohydrate-binding module (CBM1). Importantly, the novel structure of NcLPMO9C enabled a comparative study, revealing that the oxidative regioselectivity of LPMO9s (C1, C4, or both) correlates with distinct structural features of the copper coordination sphere. In strictly C1-oxidizing LPMO9s, access to the solvent-facing axial coordination position is restricted by a conserved tyrosine residue, whereas access to this same position seems unrestricted in C4-oxidizing LPMO9s. LPMO9s known to produce a mixture of C1- and C4-oxidized products show an intermediate situation.

Elucidating thermodynamic parameters for electron transfer proteins using isothermal titration calorimetry: application to the nitrogenase Fe protein

Establishing thermodynamic parameters for electron transfer reactions involving redox proteins is essential for a complete description of these important reactions. While various methods have been developed for measuring the Gibbs free energy change (Delta G(HR) or E(m)) for the protein half-reactions, deconvolution of the respective contributions of enthalpy (Delta H(HR)) and entropy (Delta S(HR)) changes is much more challenging. In the present work, an approach is developed using isothermal titration calorimetry (ITC) that allows accurate determination of all of these thermodynamic parameters for protein electron transfer half-reactions. The approach was validated for essentially irreversible and reversible electron transfer reactions between well-characterized mediators and between mediators and the protein cytochrome c. In all cases, the measured thermodynamic parameters were in excellent agreement with parameters determined by electrochemical methods. Finally, the calorimetry approach was used to determine thermodynamic parameters for electron transfer reactions of the nitrogenase Fe protein [4Fe-4S](2+/+) couple in the absence or presence of MgADP or MgATP. The E(m) value was found to change from -290 mV in the absence of nucleotides to -381 mV with MgATP and -423 mV with MgADP, consistent with earlier values. For the first time, the enthalpy (Delta H(HR)) and entropy (Delta S(HR)) contributions for each case were established, revealing shifts in the contribution of each thermodynamic parameter induced by nucleotide binding. The results are discussed in the context of current models for electron transfer in nitrogenase.

Use of stopped-flow spectrophotometry to establish midpoint potentials for redox proteins

Stopped-flow spectrophotometry was examined as a tool to assign midpoint potentials to protein redox half-reactions. The method involves the rapid mixing of protein and electron transfer mediator solutions and the determination of the absorbance of at least one of the reacting species or products at equilibrium. The utility of the method was demonstrated with two different redox proteins (nitrogenase iron protein and cytochrome c) with very different midpoint potentials. The overall errors ranged from about +/-0.5 to 3 mV. Advantages of the method include short times required for the experiments, the precision and accuracy of the method in comparison to other methods, the conservative use of valuable protein in the experiments and the ease of obtaining midpoint potentials for redox protein half-reactions, and the potential range covered by a single electron transfer mediator when the method involves mediated electron transfer. It is concluded that the stopped-flow spectrophotometry should be considered the method of choice for determining protein midpoint potentials.