The H93G Myoglobin Cavity Mutant as a Versatile Scaffold for Modeling Heme Iron Coordination Structures in Protein Active Sites and Their Characterization with Magnetic Circular Dichroism Spectroscopy

Preparation of heme model complexes is a challenging subject of long-standing interest for inorganic chemists. His93Gly sperm whale myoglobin (H93G Mb) has the proximal His replaced with the much smaller non-coordinating Gly. This leaves a cavity on the proximal side of the heme into which a wide variety of exogenous ligands can be delivered. The end result is a remarkably versatile scaffold for the preparation of model heme adducts to mimic the heme iron coordination structure of native heme proteins. In this review, we first summarize the quantitative evidence for differential ligand binding affinities of the proximal and distal pockets of the H93G Mb cavity mutant that facilitates the preparation of mixed-ligand derivatives. Then we review our use of magnetic circular dichroism and electronic absorption spectroscopy to characterize nitrogen-, oxygen-, and sulfur-donor-ligated H93G Mb adducts with an emphasis on species not easily prepared by other heme model system approaches and those that serve as spectroscopic models for native heme proteins.     

Regulating the Coordination State of a Heme Protein by a Designed Distal Hydrogen-Bonding Network

Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.     

Influence of the distal his in imparting imidazolate character to the proximal his in heme peroxidase: (1)h NMR spectroscopic study of cyanide-inhibited his42-->ala horseradish peroxidase

The functional higher oxidation states of heme peroxidases have been proposed to be stabilized by the significant imidazolate character of the proximal His. This is induced by a "push-pull" combination effect produced by the proximal Asp that abstracts ("pulls") the axial His ring N(delta)H, along with the distal protonated His that contributes ("pushes") a strong hydrogen bond to the distal ligand. The molecular and electronic structure of the distal His mutant of cyanide-inhibited horseradish peroxidase, H42A-HRPCN, has been investigated by NMR. This complex is a valid model for the active site hydrogen-bonding network of HRP compound II. The (1)H and (15)N NMR spectral parameters characterize the relative roles of the distal His42 and proximal Asp247 in imparting imidazolate character to the axial His. 1D/2D spectra reveal a heme pocket molecular structure that is highly conserved in the mutant, except for residues in the immediate proximity of the mutation. This conserved structure, together with the observed dipolar shifts of numerous active site residue protons, allowed a quantitative determination of the orientation and anisotropies of the paramagnetic susceptibility tensor, both of which are only minimally perturbed relative to wild-type HRPCN. The quantitated dipolar shifts allowed the factoring of the hyperfine shifts to reveal that the significant changes in hyperfine shifts for the axial His and ligated (15)N-cyanide result primarily from changes in contact shifts that reflect an approximately one-third reduction in the axial His imidazolate character upon abolishing the distal hydrogen-bond to the ligated cyanide. Significant changes in side chain orientation were found for the distal Arg38, whose terminus reorients to partially fill the void left by the substituted His42 side chain. It is concluded that 1D/2D NMR can quantitate both molecular and electronic structural changes in cyanide-inhibited heme peroxidase and that, while both residues contribute, the proximal Asp247 is more important than the distal His42 in imparting imidazole character to the axial His 170.     

Free-energy barriers in MbCO rebinding

The rebinding of CO to myoglobin (Mb) from locations around the active site is studied using a combination of molecular dynamics and stochastic simulations for native and L29F mutant Mb. The interaction between the dissociated ligand and the protein environment is described by the recently developed fluctuating three-point charge model for the CO molecule. Umbrella sampling along trajectories, previously found to sample the binding site (B) and the Xe4 pocket, is used to construct free-energy profiles for the ligand escape. On the basis of the Smoluchowski equation, the relaxation of different initial population distributions is followed in space and time. For native Mb at room temperature, the calculated rebinding times are in good agreement with experimental values and give an inner barrier of 4.3 kcal/mol between the docking site B (Mb...CO) and the A state (bound MbCO), compared to an effective barrier, Heff, of 4.5 kcal/mol and barriers into the majority conformation A1 and the minority conformation A3 of 2.4 and 4.3 kcal/mol, respectively. In the case of the L29F mutant, the free-energy surface is flatter and the dynamics is much more rapid. As was found in experiment, escape to the Xe4 pocket is facile for L29F whereas, for native Mb, the barriers to this site are larger. At lower temperatures, the rebinding dynamics is delayed by orders of magnitude also due to increased barriers between the docking sites.     

New Protein Footprinting: Fast Photochemical Iodination Combined with Top-Down and Bottom-Up Mass Spectrometry

We report a new approach for the fast photochemical oxidation of proteins (FPOP) whereby iodine species are used as the modifying reagent. We generate the radicals by photolysis of iodobenzoic acid at 248 nm; the putative iodine radical then rapidly modifies the target protein. This iodine-radical labeling is sensitive, tunable, and site-specific, modifying only histidine and tyrosine residues in contrast to OH radicals that modify 14 amino-acid side chains. We iodinated myoglobin (Mb) and apomyoglobin (aMb) in their native states and analyzed the outcome by both top-down and bottom-up proteomic strategies. Top-down sequencing selects a certain level (addition of one I, two I's) of modification and determines the major components produced in the modification reaction, whereas bottom-up reveals details for each modification site. Tyr146 is found to be modified for aMb but less so for Mb. His82, His93, and His97 are at least 10 times more modified for aMb than for Mb, in agreement with NMR studies. For carbonic anhydrase and its apo form, there are no significant differences of the modification extents, indicating their similarity in conformation and providing a control for this approach. For lispro insulin, insulin-EDTA, and insulin complexed with zinc, iodination yields are sensitive to differences in insulin oligomerization state. The iodine radical labeling is a promising addition to protein footprinting methods, offering higher specificity and lower reactivity than ?OH and SO(4)(-?), two other radicals already employed in FPOP.     

Ligand dynamics in myoglobin: calculation of infrared spectra for photodissociated NO.

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.     

Dynamics of nitric oxide rebinding and escape in horseradish peroxidase

Ultrafast kinetic measurements of NO rebinding to horseradish peroxidase (HRP) are reported for the first time. The geminate kinetics are found to be exponential for all HRP samples studied. The ferric forms of HRP have NO geminate recombination time constants in the range of 15-30 ps, while the ferrous form has a time constant of approximately 7 ps. The simple exponential NO geminate kinetics found for HRP demonstrate that heme relaxation is not the underlying source of the nonexponential NO rebinding in myoglobin (Mb). The NO ligand escape rates from HRP are also determined, and they are found to depend dramatically on the presence or absence of the competitive inhibitor benzohydroxamic acid (BHA). The kinetic results indicate that, in contrast to Mb, there is direct solvent access to the distal heme pocket of HRP.     

甲烷氧化菌素-铜配合物催化过氧化氢氧化对苯二酚

为了探讨甲烷氧化菌素(Mb)-铜配合物(Mb-Cu)模拟过氧化物酶的可行性, 利用HP20大孔树脂、 Supelco LC-C₁₈固相萃取和固定化金属亲和层析从甲基弯菌IMV3011中分离纯化得到Mb. 铬天青比色法显示Mb具有铜亲和性. 通过液相色谱-飞行时间质谱联用仪、 紫外光谱和荧光光谱对Mb结构进行了表征. 使用Mb-Cu配合物作为过氧化物酶模拟物, 利用紫外-可见分光光度法研究了Mb-Cu催化过氧化氢氧化对苯二酚的动力学. 考察了体系温度、 Mb-Cu添加量及过氧化氢浓度对催化反应的影响, 发现Mb-Cu符合生物催化剂条件影响的一般规律, 但比生物酶具有更高的热稳定性. 研究结果表明, Mb-Cu可作为催化氧化对苯二酚的过氧化物酶模拟酶.     

Functional tuning and expanding of myoglobin by rational protein design

Rational protein design is a powerful strategy, not only for revealing the structure and function relationship of natural metallo-proteins, but also for creating artificial metalloproteins with improved properties and functions. Myoglobin (Mb), a small heme protein created by nature with diverse functions, has been shown to be an ideal scaffold for rational protein design. The progress reviewed herein includes fine-tuning its native functions of O₂ binding and transport, peroxidase activity and nitrite reductase (NIR) activity, and rational expanding its functionalities to peroxygenase, heme-copper oxidase (HCO), nitric oxide reductase (NOR), as well as hydroxylamine reductase. These studies have enhanced our understanding of how metalloproteins work in nature, and provided insights for rational design of functional metalloproteins for practical applications in the future.     

HNO binding in a heme protein: structures, spectroscopic properties, and stabilities

HNO can interact with numerous heme proteins, but atomic level structures are largely unknown. In this work, various structural models for the first stable HNO heme protein complex, MbHNO (Mb, myoglobin), were examined by quantum chemical calculations. This investigation led to the discovery of two novel structural models that can excellently reproduce numerous experimental spectroscopic properties. They are also the first atomic level structures that can account for the experimentally observed high stabilities. These two models involve two distal His conformations as reported previously for MbCNR and MbNO. However, a unique dual hydrogen bonding feature of the HNO binding was not reported before in heme protein complexes with other small molecules such as CO, NO, and O(2). These results shall facilitate investigations of HNO bindings in other heme proteins.     

Electrochemical and spectroelectrochemical properties of manganese reconstituted myoglobin

Electrochemical and spectroelectrochemical properties of manganese(III) reconstituted myoglobin (Mn(III)–Mb) have been investigated. No redox wave of Mn(III)–Mb was observed at a highly hydrophilic indium oxide electrode on which rapid direct electron transfer of native myoglobin took place, suggesting the electron transfer reaction of Mn(III)–Mb at an indium oxide electrode is very slow. The rate constant of the chemical reduction of Mn(III)–Mb with dithionite was ca. 20 times smaller than that of native Mb. Using an optically transparent thin layer electrode (OTTLE) cell and Oxazine-170 perchlorate, 5,9-bis(diethylamino)-10-methyl-benzo[a]phenoxazonium perchlorate, as an electron transfer mediator, the redox potential for the Mn(III) Mn(II)–Mb couple was estimated to be −0.32 V versus Ag AgCl (sat. KCl) at 25°C.     

Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids

Metalloproteins have inspired chemists for many years to synthesize artificial catalysts that mimic native enzymes.As a complementary approach to studying native enzymes or making synthetic models,biosynthetic approach using small and stable proteins to model native enzymes has offered advantages of incorporating non-covalent secondary sphere interactions under physiological conditions.However,most biosynthetic models are restricted to natural amino acids.To overcome this limitation,incorporating unnatural amino acids into the biosynthetic models has shown promises.In this review,we summarize first synthetic,semisynthetic and biological methods of incorporates unnatural amino acids(UAAs)into proteins,followed by progress made in incorporating UAAs into both native metalloproteins and their biosynthetic models to fine-tune functional properties beyond native enzymes or their variants containing natural amino acids,such as reduction potentials of azurin,O_2 reduction rates and percentages of product formation of HCO models in Mb,the rate of radical transport in ribonucleotide reductase(RNR)and the proton and electron transfer pathways in photosystemⅡ(PSⅡ).We also discuss how this endeavour has allowed systematic investigations of precise roles of conserved residues in metalloproteins,such as Metl21 in azurin,Tyr244 that is cross-linked to one of the three His ligands to CuB in HCO,Tyr122,356,730 and 731 in RNR and TyrZ in PSⅡ.These examples have demonstrated that incorporating UAAs has provided a new dimension in our efforts to mimic native enzymes and in providing deeper insights into structural features responsible high enzymatic activity and reaction mechanisms,making it possible to design highly efficient artificial catalysts with similar or even higher activity than native enzymes.     

肌红蛋白-壳聚糖-金胶纳米复合修饰电极的电催化

在pH 5.4的HAc-NaAc缓冲溶液中,肌红蛋白-壳聚糖-金胶薄膜修饰电极(Mb-Ch itosan-Au colloid/GCE)于-0.20 V(vs.Ag/AgC l)处有一对准可逆的氧化还原峰,即Mb血红素辅基Fe(Ⅲ)/Fe(Ⅱ)电对的特征峰.本实验条件下,肌红蛋白与玻碳电极之间的电子传递明显加快,并考察了扫速、溶液pH及支持电解质浓度等因素对肌红蛋白电子传递的影响.紫外光谱图表明:肌红蛋白在壳聚糖-金胶溶液中依然保持其原始构象.该肌红蛋白-壳聚糖-金胶纳米修饰电极还能电催化溶解氧的还原.     

Myoglobin/sol-gel film modified electrode: direct electrochemistry and electrochemical catalysis

Direct electrochemical and electrocatalytic behavior of myoglobin (Mb) immobilized on carbon paste electrode (CPE) by a silica sol-gel film derived from tetraethyl orthosilicate was investigated for the first time. Mb/sol-gel film modified electrodes show a pair of well-defined and nearly reversible cyclic voltammetric peaks for the Mb Fe(III)/Fe(II) redox couple at about -0.298 V (vs Ag/AgCl) in a pH 7.0 phosphate buffer solution. The formal potential of the Mb heme Fe(III)/Fe(II) couple shifted linearly with pH with a slope of 52.4 mV/pH, denoting that an electron transfer accompanies single-proton transportation. An FTIR and UV-vis spectroscopy study confirms that the secondary structure of Mb immobilized on an electrode by a sol-gel film still maintains the original arrangement. The immobilized Mb displays the features of a peroxidase and acts in an electrocatalytic manner in the reduction of oxygen, trichloroacetic acid (TCA), and nitrite. In comparison to other electrodes, the chemically modified electrodes used in this study for direct electrochemistry and electrocatalysis of Mb are easy to fabricate and fairly inexpensive. Consequently, the Mb/sol-gel film modified electrode provides a convenient way to perform electrochemical research on this kind of protein. It also has potential use in the fabrication of bioreactors and third-generation biosensors.     

苏丹红Ⅱ与肌红蛋白相互作用的分子模拟与实验

用荧光光谱法研究了苏丹红Ⅱ与肌红蛋白(Mb)之间的相互作用, 实验结果表明,二者结合位点数近似为1, 结合常数K=3.84×107L/mol, 有很强的相互作用. 用分子柔性对接技术模拟确定了它们之间的作用位点、作用力类型及相互作用能. 理论计算的结果表明,苏丹红Ⅱ和Mb相互作用的势能为-9419.9 kJ/mol, 静电能为-7468.8 kJ/mol, 范德华能为-1951.0 kJ/mol. 苏丹红Ⅱ与Mb中His64残基形成氢键, 苏丹红Ⅱ也能与疏水氨基酸残基, 如能产生内源荧光的Phe33、Phe43、Phe106 和 Phe138等发生作用, 这与苏丹红Ⅱ能使Mb荧光猝灭的实验结果是一致的.     

Temperature-dependent studies of NO recombination to heme and heme proteins

The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.     

酸诱导拥挤条件下肌红蛋白及突变体去折叠过程

采用紫外-可见吸收光谱、同步荧光光谱和圆二色(CD)光谱法研究拥挤试剂葡聚糖70 (Dextran70)和聚蔗糖70 (Ficoll70)存在条件下, 酸诱导野生型肌红蛋白Mb(WT)及其突变体Mb(D60K)的去折叠过程. 结果显示: 在Dextran70 和Ficoll70 两种拥挤环境下, Mb(WT)的变性中点pH值由4.25 分别降低到3.78 与3.76, 拥挤试剂加入后增强了Mb(WT)的耐酸能力; 肌红蛋白60位天冬氨酸(Asp)突变为赖氨酸(Lys)后, 变性中点pH值由4.25 降低到4.19, 耐酸性比野生型肌红蛋白有所增强, Mb(D60K)在Dextran70 和Ficoll70 两种拥挤环境下变性中点pH值由4.19 分别降至3.74 和3.12. 以上实验说明肌红蛋白表面氨基酸突变和拥挤试剂的添加起到了稳定血红素微环境、芳香族氨基酸及二级结构和保护蛋白天然状态的作用.     

Electrochemical performance and electrocatalytic behavior of myoglobin on graphene tube-modified electrode

A new protein biosensing strategy based on a graphene tube (GT)-modified electrode was developed in this article. GT as a fixed material and signal amplifier was loaded on the carbon ionic liquid electrode (CILE) surface, which could provide a suitable environment for myoglobin (Mb) immobilization and promote electron transfer between Mb and the electrode. Fourier-transform infrared spectroscopy (FT-IR) of Mb before and after mixing with GT was checked and showed that the native structure of Mb was maintained. The direct electrochemistry of Mb was investigated with a pair of obtained well-defined and quasireversible redox peaks. The modified electrode (Nafion/Mb/GT/CILE) also showed excellent electrocatalytic activity for the reduction of trichloroacetic acid (TCA) and NaNO₂, which could be utilized to determine the concentrations of TCA and NaNO₂ with wide detection range and low detection limit. The biosensor was further applied to the detection of a real sample and obtained satisfactory experimental results.     

Direct electrochemistry and electrocatalysis of myoglobin immobilized on L-cysteine self-assembled gold electrode

Myoglobin (Mb) has been successfully immobilized on a self-assembled monolayer (SAM) of L-cysteine (Cys) on a gold electrode, Au/Cys. The presence of a pair of well-defined and nearly reversible waves centered at ca. 0.086 V vs Ag/AgCl (pH 6.5) suggests that the native character of Mb heme Fe(III/II) redox couple has been obtained. The formal potential of Mb on Cys SAM exhibited pH-dependent variation in the pH range of 5-9 with a slope of 55 mV/pH, indicating that the electron transfer is accompanied by a single proton exchange. Thermodynamic and kinetic aspects of Mb adsorption processes on Au/Cys were studied by using voltammetric and quartz-crystal microbalance methods. The Au/Cys electrode with immobilized Mb exhibited electrocatalytic activity toward ascorbic acid (AA) oxidation with an overpotential decrease of over 400 mV and a linear dependence of current on the AA concentration from 0.5 to 5.0 mmol L(-1).     

Fabrication of electroactive layer-by-layer films of myoglobin with gold nanoparticles of different sizes

Alternate adsorption of oppositely charged myoglobin (Mb) and gold nanoparticles with different sizes were used to assemble {Au/Mb}n layer-by-layer films on solid surfaces by electrostatic interaction between them. The direct electrochemistry of Mb was realized in {Au/Mb}n films at pyrolytic graphite (PG) electrodes, showing a pair of well-defined, nearly reversible cyclic voltammetry (CV) peaks for the Mb heme FeIII/FeII redox couple. Quartz crystal microbalance (QCM), electrochemical impedance spectroscopy (EIS), and CV were used to monitor or confirm the growth of the films. Compared with other Mb layer-by-layer films with nonconductive nanoparticles or polyions, {Au/Mb}n films showed much improved properties, such as smaller electron-transfer resistance (Rct) measured by EIS with Fe(CN)3-/4- redox probe, higher maximum surface concentration of electroactive Mb (Gamma*max), and better electrocatalytic activity toward reduction of O2 and H2O2, mainly because of the good conductivity of Au nanoparticles. Because of the high biocompatibility of Au nanoparticles, adsorbed Mb in the films retained its near native structure and biocatalytic activity. The size effect of Au nanoparticles on the electrochemical and electrocatalytic activity of Mb in {Au/Mb}n films was investigated, demonstrating that the {Au/Mb}n films assembled with smaller-sized Au nanoparticles have smaller Rct, higher Gamma*max, and better biocatalytic reactivity than those with larger size.