AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking

E.coli AlkB is a direct DNA/RNA repair protein that oxidatively reverses N1 alkylated purines and N3 alkylated pyrimidines to regular bases.Previous crystal structures have revealed N1-methyl adenine(1-meA) recognition by AlkB and a unique base flipping mechanism,but how the AlkB active site can accommodate bulky base adducts is largely unknown.Employing a previously developed chemical cross-linking technique,we crystallized AlkB with a duplex DNA containing a caged thymine base(cagedT).The structure reveal...     

Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking

Engineering chemical cross-linking groups at the protein/DNA interface provide a powerful method for probing the putative active site and a damage searching mechanism of the Escherichia coli alkylation DNA repair protein AlkB.     

Local and global effects of metal binding within the small subunit of ribonucleotide reductase

Each beta-protomer of the small betabeta subunit of Escherichia coli ribonucleotide reductase (R2) contains a binuclear iron cluster with inequivalent binding sites: Fe(A) and Fe(B). In anaerobic Fe(II) titrations of apoprotein under standard buffer conditions, we show that the majority of the protein binds only one Fe(II) atom per betabeta subunit. Additional iron occupation can be achieved upon exposure to O2 or in high glycerol buffers. The differential binding affinity of the A- and B-sites allows us to produce heterobinuclear Mn(II)Fe(II) and novel Mn(III)Fe(III) clusters within a single beta-protomer of R2. The oxidized species are produced with H2O2 addition. We demonstrate that no significant exchange of metal occurs between the A- and B-sites, and thus the binding of the first metal is under kinetic control, as has been suggested previously. The binding of first Fe(II) atom to the active site in a beta-protomer (betaI) induces a global protein conformational change that inhibits access of metal to the active site in the other beta-protomer (betaII). The binding of the same Fe(II) atom also induces a local effect at the active site in betaI-protomer, which lowers the affinity for metal in the A-site. The mixed metal FeMn species are quantitatively characterized with electron paramagnetic resonance spectroscopy. The previously reported catalase activity of Mn2(II)R2 is shown not to be associated with Mn.     

Calculations on the structure and spectral properties of cytochrome c551 using DFT and ONIOM methods

The active site geometry of cytochrome (Cyt) c(551) and its mutated form containing Fe(II) and Fe(III) ions have been calculated using density functional theory (DFT)-based Becke's three-parameter hybrid exchange and Lee-Yang-Parr correlation (B3LYP) method. In addition, calculations have also been carried out using hybrid meta DFT-based M06 functional. The effect of the protein milieu on the active site geometry has also been probed using two-layer via our own N-layered integrated molecular orbital + molecular mechanics (ONIOM) method. Evidence from the calculations reveal that the active site geometry is not significantly affected by the oxidation state of metal ion. The difference in the geometry of the active site and that of the same with the entire protein environment is only minimal, which shows that the protein milieu does not influence the structure of the active site. The calculated electronic transition energies from the time-dependent DFT (TDDFT) calculations are in close agreement with the experimental values. Although there are no significant variations in the active site geometry upon oxidation, the changes in the electronic transition energies have been attributed to the reduction in the overlap of metal ion with the ligand orbitals. In addition, it is found that mutation does not influence the active site geometry and the electronic transition energies. Nevertheless, mutation leads to the formation of more compact structure than the native Cyt c(551).     

Synthetic models of the reduced active site of superoxide reductase

We report the synthesis, structural and spectroscopic characterization, and magnetic and electrochemical studies of a series of iron(II) complexes of the pyridyl-appended diazacyclooctane ligand L(8)py(2), including several that model the square-pyramidal [Fe(II)(N(his))(4)(S(cys))] structure of the reduced active site of the non-heme iron enzyme superoxide reductase. Combination of L(8)py(2) with FeCl(2) provides [L(8)py(2)FeCl(2)] (1), which contains a trigonal-prismatic hexacoordinate iron(II) center, whereas a parallel reaction using [Fe(H(2)O)(6)](BF(4))(2) provides [L(8)py(2)Fe(FBF(3))]BF(4) (2), a novel BF(4)(-)-ligated square-pyramidal iron(II) complex. Substitution of the BF(4)(-) ligand in 2 with formate or acetate ions affords distorted pentacoordinate [L(8)py(2)Fe(O(2)CH)]BF(4) (3) and [L(8)py(2)Fe(O(2)CCH(3))]BF(4) (4), respectively. Models of the superoxide reductase active site are prepared upon reaction of 2 with sodium salts of aromatic and aliphatic thiolates. These model complexes include [L(8)py(2)Fe(SC(6)H(4)-p-CH(3))]BF(4) (5), [L(8)py(2)Fe(SC(6)H(4)-m-CH(3))]BF(4) (6), and [L(8)py(2)Fe(SC(6)H(11))]BF(4) (7). X-ray crystallographic studies confirm that the iron(II)-thiolate complexes model the square-pyramidal geometry and N(4)S donor set of the reduced active site of superoxide reductase. The iron(II)-thiolate complexes are high spin (S = 2), and their solutions are yellow in color because of multiple charge-transfer transitions that occur between 300 and 425 nm. The ambient temperature cyclic voltammograms of the iron(II)-thiolate complexes contain irreversible oxidation waves with anodic peak potentials that correlate with the relative electron donating abilities of the thiolate ligands. This electrochemical irreversibility is attributed to the bimolecular generation of disulfides from the electrochemically generated iron(III)-thiolate species.     

Simultaneous spectrophotometric determination of nickel and iron in copper-base alloy with bromo-PADAP

The reaction of nickel (II) with Br-PADAP, in the presence of tergitol NPX surfactant, forms a complex with absorption peaks at 520 and 560 nm. The iron(II)-Br-PADAP system at the same conditions forms a chelate with absorption peaks at 560 and 748 nm. This allows the simultaneous spectrophotometric determination of nickel and iron by measuring the absorbance at 560 and 748 nm. The proposed method, at ph 4.0-5.7, shows a molar absorptivity of 1.22 x 10(5)l . mole(-1) . cm(-1) for nickel at 560 nm and 8.20 x 10(4)l . mole(-1) . cm(-1) at 560 nm and 3.35 x 10(4)l . mole(-1) . cm(-1) at 748 nm for iron(II). Beer's law is obeyed up to 0.40 mu/ml of nickel(II) and up to 0.65 mu/ml of iron(II). Thiosulphate as masking agent allows the simultaneous determination of iron and nickel in the presence of high concentrations of copper. The ethylene glycol 2-(2-amino-ethyl) tetracetic acid provides the elimination of many other interferences. The method has been applied successfully to the simultaneous determination of nickel and iron in reference samples.     

Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study

The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their M?ssbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe M?ssbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous M?ssbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.     

Refining the active site structure of iron-iron hydrogenase using computational infrared spectroscopy

Iron-iron hydrogenases ([FeFe]H2ases) are exceptional natural catalysts for the reduction of protons to dihydrogen. Future biotechnological applications based on these enzymes require a precise understanding of their structures and properties. Although the [FeFe]H2ases have been characterized by single-crystal X-ray crystallography and a range of spectroscopic techniques, ambiguities remain regarding the details of the molecular structures of the spectroscopically observed forms. We use density functional theory (DFT) computations on small-molecule computational models of the [FeFe]H2ase active site to address this problem. Specifically, a series of structural candidates are geometry optimized and their infrared (IR) spectra are simulated using the computed C-O and C-N stretching frequencies and infrared intensities. Structural assignments are made by comparing these spectra to the experimentally determined IR spectra for each form. The H red form is assigned as a mixture of an Fe(I)Fe(I) form with an open site on the distal iron center and either a Fe(I)Fe(I) form in which the distal cyanide has been protonated or a Fe(II)Fe(II) form with a bridging hydride ligand. The Hox form is assigned as a valence-localized Fe(I)Fe(II) redox level with an open site at the distal iron. The Hox(air)(ox) form is assigned as an Fe(II)Fe(II) redox level with OH(-) or OOH(-) bound to the distal iron center that may or may not have an oxygen atom bound to one of the sulfur atoms of the dithiolate linker. Comparisons of the computed IR spectra of the (12)CO and (13)CO inhibited form with the experimental IR spectra show that exogenous CO binds terminally to the distal iron center.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

Fe3(CO)12与P(NEt2)2Cl的反应--两核和三核铁羰基簇合衍生物的合成和晶体结构

Fe_3(CO)_(12)与配位基前体P(NEt_2)_2Cl反应,给出4个新的两核和三核铁羰基簇合衍生物:Fe_2(CO)_6(μ-Cl)[μ-P(NEt_2)_2](Ⅰ),Fe_2(CO)_6[μ-P(NEt_2)_2]_2(Ⅱ),Fe_3(CO)_9(μ-CO)(μ_3-PNEt_2)(Ⅲ)和Fe_3(CO)_9(μ_3-PNEt_2)[P(NEt_2)_3](Ⅳ)。在反应期间,配前体分子中的P-Cl和P-N键劈开,形成的分子片Cl、PNEt_2、P(NEt_2)_2和P(NEt_2)_3作为配体与铁羰合物重新组建成上述簇合物。利用X射线衍射法测定了它们的晶体结构。Ⅰ属三斜晶系,P1空间群,晶胞参数a=0.8745(6)nm,b=0.9601(7)nm,c=1.3996(10)nm,α=74.131(11)°,β=79.480(12)°,γ=69.727(12)°,V=1.0553(13)nm~3,D_c=1.543g·cm~(-3),Z=2,R=0.0443,wR=0.0831。Ⅱ属正交晶系,Pbcn空间群,晶胞参数a=1.0153(3)nm,b=1.7543(5)nm,c=1.6860(5)nm,V=3.0031(15)nm~3,D_c=1.394g·cm~(-3),Z=4,R=0.0519,wR=0.1035。Ⅲ属单斜晶系,P2_1/c空间群,晶胞参数a=1.0280(5)nm,b=1.2113(5)nm,c=1.9192(7)nm,β=93.560(7)°,V=2.1366(16)nm~3,D_c=1.712g·cm~(-3),Z=4。Ⅳ属单斜晶系,Cc空间群,晶胞参数a=1.5875(7)nm,b=1.0359(5)nm,C=2.1919(9)nm,β=101.266(8)°,V=3.535(3)nm~3,Dc=1.443g·cm~(-3),Z=4。Ⅰ和Ⅱ为两核铁簇,其簇骨架Fe_2PCl和Fe_2P_2呈蝶状。Ⅲ和Ⅳ     

Spectroscopic definition of the ferroxidase site in M ferritin: comparison of binuclear substrate vs cofactor active sites

Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a nonheme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly antiferromagnetically coupled, consistent with a mu-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure--including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin--coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites.     

Study of the VirE2-ssT-DNA complex formation by scanning probe microscopy and gel electrophoresis- T-complex visualization.

The recombinant virulence protein VirE2, capable of forming a complex with single-stranded T-DNA during transfer into plant cells, was isolated, purified, and used for interactions with ssT-DNA. The in vitro interaction of VirE2 and ss-binding protein from Escherichia coli with single-stranded DNA (phage lambda) was determined by agarose gel electrophoresis by the formation of high-molecular-weight complexes after preliminary coincubation of purified protein preparations with ssDNA. We show that VirE2 binds to single-stranded DNA and protects it against nuclease S1 degradation much better than does E. coli SSB protein. We for first time observed the VirE2-ssT-DNA complex by using atomic force microscopy. The complex observed by atomic force microscopy after ssT-DNA and VirE2 protein mixing has a length of about 800 nm and a 5-8 nm width in sites with attached VirE2 protein.     

Photoenhanced oxidative DNA cleavage with non-heme iron(II) complexes

The DNA cleavage activity of iron(II) complexes of a series of monotopic pentadentate N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine (N4Py)-derived ligands (1-5) was investigated under laser irradiation at 473, 400.8, and 355 nm in the absence of a reducing agent and compared to that under ambient lighting. A significant increase in activity was observed under laser irradiation, which is dependent on the structural characteristics of the complexes and the wavelength and power of irradiation. Under photoirradiation at 355 nm, direct double-stand DNA cleavage activity was observed with Fe(II)-1 and Fe(II)-3-5, and a 56-fold increase in the single-strand cleavage activity was observed with Fe(II)-2. Mechanistic investigations revealed that O(2)(?-), (1)O(2), and OH(?) contribute to the photoenhanced DNA cleavage activity, and that their relative contribution is dependent on the wavelength. It is proposed that the origin of the increase in activity is the photoenhanced formation of an Fe(III)OOH intermediate as the active species or precursor.     

Formation of a stable cyano-bridged dinuclear iron cluster following oxidation of the superoxide reductases from Treponema pallidum and Desulfovibrio vulgaris with K(3)Fe(CN)(6)

Superoxide reductases catalyze the monovalent reduction of superoxide anion to hydrogen peroxide. Spectroscopic evidence for the formation of a dinuclear cyano-bridged adduct after K(3)Fe(CN)(6) oxidation of the superoxide reductases neelaredoxin from Treponema pallidum and desulfoferrodoxin from Desulfovibrio vulgaris was reported. Oxidation with K(3)Fe(CN)(6) reveals a band in the near-IR with lambda(max) at 1020 nm, coupled with an increase of the iron content by almost 2-fold. Fourier transform infrared spectroscopy provided additional evidence with CN-stretching vibrations at 2095, 2025-2030, and 2047 cm(-)(1), assigned to a ferrocyanide adduct of the enzyme. Interestingly, the low-temperature electronic paramagnetic resonance (EPR) spectra of oxidized TpNlr reveal at least three different species indicating structural heterogeneity in the coordination environment of the active site Fe ion. Given the likely 6-coordinate geometry of the active site Fe(3+) ion in the ferrocyanide adduct, we propose that the rhombic EPR species can serve as a model of a hexacoordinate form of the active site.     

Rational tuning of the thiolate donor in model complexes of superoxide reductase: direct evidence for a trans influence in Fe(III)-OOR complexes

Iron peroxide species have been identified as important intermediates in a number of nonheme iron as well as heme-containing enzymes, yet there are only a few examples of such species either synthetic or biological that have been well characterized. We describe the synthesis and structural characterization of a new series of five-coordinate (N4S(thiolate))Fe(II) complexes that react with tert-butyl hydroperoxide ((t)BuOOH) or cumenyl hydroperoxide (CmOOH) to give metastable alkylperoxo-iron(III) species (N4S(thiolate)Fe(III)-OOR) at low temperature. These complexes were designed specifically to mimic the nonheme iron active site of superoxide reductase, which contains a five-coordinate iron(II) center bound by one Cys and four His residues in the active form of the protein. The structures of the Fe(II) complexes are analyzed by X-ray crystallography, and their electrochemical properties are assessed by cyclic voltammetry. For the Fe(III)-OOR species, low-temperature UV-vis spectra reveal intense peaks between 500-550 nm that are typical of peroxide to iron(III) ligand-to-metal charge-transfer (LMCT) transitions, and EPR spectroscopy shows that these alkylperoxo species are all low-spin iron(III) complexes. Identification of the vibrational modes of the Fe(III)-OOR unit comes from resonance Raman (RR) spectroscopy, which shows nu(Fe-O) modes between 600-635 cm(-1) and nu(O-O) bands near 800 cm(-1). These Fe-O stretching frequencies are significantly lower than those found in other low-spin Fe(III)-OOR complexes. Trends in the data conclusively show that this weakening of the Fe-O bond arises from a trans influence of the thiolate donor, and density functional theory (DFT) calculations support these findings. These results suggest a role for the cysteine ligand in SOR, and are discussed in light of the recent assessments of the function of the cysteine ligand in this enzyme.     

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to their substrate specificity. Swapping such active‐site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X‐ray structures and enzyme kinetics suggests a role of the active‐site residues in substrate recognition. Such a divergent active‐site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.     

Geometric and electronic structure studies of the binuclear nonheme ferrous active site of toluene-4-monooxygenase: parallels with methane monooxygenase and insight into the role of the effector proteins in O2 activation

Multicomponent monooxygenases, which carry out a variety of highly specific hydroxylation reactions, are of great interest as potential biocatalysts in a number of applications. These proteins share many similarities in structure and show a marked increase in O2 reactivity upon addition of an effector component. In this study, circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD have been used to gain spectroscopic insight into the Fe(II)Fe(II) active site in the hydroxylase component of Toluene-4 monoxygenase (T4moH) and the complex of T4moH bound by its effector protein, T4moD. These results have been correlated to spectroscopic data and density functional theory (DFT) calculations on MmoH and its interaction with MmoB. Together, these data provide further insight into the geometric and electronic structure of these biferrous active sites and, in particular, the perturbation associated with component B/D binding. It is found that binding of the effector protein changes the geometry of one iron center and orientation of its redox active orbital to accommodate the binding of O2 in a bridged structure for efficient 2-electron transfer that can form a peroxo intermediate.     

A synthetic analogue of the active site of Fe-containing nitrile hydratase with carboxamido N and thiolato S as donors: synthesis, structure, and reactivities.

As part of our work on models of the iron(III) site of Fe-containing nitrile hydratase, a designed ligand PyPSH(4) with two carboxamide and two thiolate donor groups has been synthesized. Reaction of (Et(4)N)[FeCl(4)] with the deprotonated form of the ligand in DMF affords the mononuclear iron(III) complex (Et(4)N)[Fe(III)(PyPS)] (1) in high yield. The iron(III) center is in a trigonal bipyramidal geometry with two deprotonated carboxamido nitrogens, one pyridine nitrogen, and two thiolato sulfurs as donors. Complex 1 is stable in water and binds a variety of Lewis bases at the sixth site at low temperature to afford green solutions with a band around 700 nm. The iron(III) centers in these six-coordinate species are low-spin and exhibit EPR spectra much like the enzyme. The pK(a) of the water molecule in [Fe(III)(PyPS)(H(2)O)](-) is 6.3 +/- 0.4. The iron(III) site in 1 with ligated carboxamido nitrogens and thiolato sulfurs does not show any affinity toward nitriles. It thus appears that at physiological pH, a metal-bound hydroxide promotes hydration of nitriles nested in close proximity of the iron center in the enzyme. Redox measurements demonstrate that the carboxamido nitrogens prefer Fe(III) to Fe(II) centers. This fact explains the absence of any redox behavior at the iron site in nitrile hydratase. Upon exposure to limited amount of dioxygen, 1 is converted to the bis-sulfinic species. The structure of the more stable O-bonded sulfinato complex (Et(4)N)[Fe(III)(PyP[SO(2)](2))] (2) has been determined. Six-coordinated low-spin cyanide adducts of the S-bonded and the O-bonded sulfinato complexes, namely, Na(2)[Fe(III)(PyP[SO(2)](2))(CN)] (4) and (Et(4)N)(2)[Fe(III)(PyP[SO(2)](2))(CN)] (5), afford green solutions in water and other solvents. The iron(II) complex (Et(4)N)(2)[Fe(II)(PyPS)] (3) has also been isolated and structurally characterized.     

Prediction of high-valent iron K-edge absorption spectra by time-dependent density functional theory

In recent years, a number of high-valent iron intermediates have been identified as reactive species in iron-containing metalloproteins. Inspired by the interest in these highly reactive species, chemists have synthesized Fe(IV) and Fe(V) model complexes with terminal oxo or nitrido groups, as well as a rare example of an Fe(VI)-nitrido species. In all these cases, X-ray absorption spectroscopy has played a key role in the identification and characterization of these species, with both the energy and intensity of the pre-edge features providing spectroscopic signatures for both the oxidation state and the local site geometry. Here we build on a time-dependent DFT methodology for the prediction of Fe K- pre-edge features, previously applied to ferrous and ferric complexes, and extend it to a range of Fe(IV), Fe(V) and Fe(VI) complexes. The contributions of oxidation state, coordination environment and spin state to the spectral features are discussed. These methods are then extended to calculate the spectra of the heme active site of P450 Compound II and the non-heme active site of TauD. The potential for using these methods in a predictive manner is highlighted.