CO rebinding to protoheme: investigations of the proximal and distal contributions to the geminate rebinding barrier

The rebinding kinetics of CO to protoheme (FePPIX) in the presence and absence of a proximal imidazole ligand reveals the magnitude of the rebinding barrier associated with proximal histidine ligation. The ligation states of the heme under different solvent conditions are also investigated using both equilibrium and transient spectroscopy. In the absence of imidazole, a weak ligand (probably water) is bound on the proximal side of the FePPIX-CO adduct. When the heme is encapsulated in micelles of cetyltrimethylammonium bromide (CTAB), photolysis of FePPIX-CO induces a complicated set of proximal ligation changes. In contrast, the use of glycerol-water solutions leads to a simple two-state geminate kinetic response with rapid (10-100 ps) CO recombination and a geminate amplitude that can be controlled by adjusting the solvent viscosity. By comparing the rate of CO rebinding to protoheme in glycerol solution with and without a bound proximal imidazole ligand, we find the enthalpic contribution to the proximal rebinding barrier, H(p), to be 11 +/- 2 kJ/mol. Further comparison of the CO rebinding rate of the imidazole bound protoheme with the analogous rate in myoglobin (Mb) leads to a determination of the difference in their distal free energy barriers: DeltaG(D) approximately 12 +/- 1 kJ/mol. Estimates of the entropic contributions, due to the ligand accessible volumes in the distal pocket and the xenon-4 cavity of myoglobin ( approximately 3 kJ/mol), then lead to a distal pocket enthalpic barrier of H(D) approximately 9 +/- 2 kJ/mol. These results agree well with the predictions of a simple model and with previous independent room-temperature measurements of the enthalpic MbCO rebinding barrier (18 +/- 2 kJ/mol).     

Analysis and characterization of the transition from the Arrhenius to non-Arrhenius structural relaxation in fragile glass-forming liquids

We have studied the transition from an Arrhenius-like to a non-Arrhenius-like structural relaxation behavior in fragile glass-forming liquids. This transition is denoted by the temperature T_A that usually occurs above the melting point T_m and the dynamic crossover temperature T_B. Recent studies reveal that T_A is a characteristic temperature related with the dynamical properties of the system. However, its unambiguous determination is not easy. In this work, a method to obtain the temperature T_A from the experimental data of α-relaxation time is presented. The obtained T_A is compared with the cooperativity onset temperature T_x extracted from the bond strength–coordination number fluctuation model. The result reveals that T_A is close to T_x for fragile liquids. From the result of the present analyses combined with the linear relation T_x \(\propto\) T₀, where T₀ is the Vogel temperature, the Arrhenius crossover phenomenon in fragile liquids is linked to the low-temperature structural relaxation dynamics.     

Docking to heme proteins

In silico screening has become a valuable tool in drug design, but some drug targets represent real challenges for docking algorithms. This is especially true for metalloproteins, whose interactions with ligands are difficult to parametrize. Our docking algorithm, EADock, is based on the CHARMM force field, which assures a physically sound scoring function and a good transferability to a wide range of systems, but also exhibits difficulties in case of some metalloproteins. Here, we consider the therapeutically important case of heme proteins featuring an iron core at the active site. Using a standard docking protocol, where the iron–ligand interaction is underestimated, we obtained a success rate of 28% for a test set of 50 heme‐containing complexes with iron‐ligand contact. By introducing Morse‐like metal binding potentials (MMBP), which are fitted to reproduce density functional theory calculations, we are able to increase the success rate to 62%. The remaining failures are mainly due to specific ligand–water interactions in the X‐ray structures. Testing of the MMBP on a second data set of non iron binders (14 cases) demonstrates that they do not introduce a spurious bias towards metal binding, which suggests that they may reliably be used also for cross‐docking studies. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

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.     

How CO binds to hexacoordinated heme in neuroglobin protein

In the present work, density functional theory (DFT) has been used to investigate CO binding to the hexacoordinated heme in neuroglobin (Ngb) protein. Structural relaxation of the selected model system in the protein environment has been fully included by the alternative quantum and molecular mechanical optimizations. The polarized continuum model (PCM) was used to simulate interaction between the model system and the protein environment. The CO binding could take place in a concerted way and a barrier of 17.9 kcal mol(-1) was predicted on the concerted singlet pathway, which is not favorable in energy. The adiabatically sequential pathway requires an energy of 14.5 kcal mol(-1) for formation of the singlet intermediate. There exist two nonadiabatic sequential pathways for the CO binding, which involves the triplet and quintet states of intermediate. Both the singlet/triplet and singlet/quintet intersections play an important role in nonadiabatic sequential processes, which enhance the probability that the processes occur. The nonadiabatic processes that involve the triplet and quintet states of intermediate are the most probable pathways for the CO binding to the hexacoordinated heme in Ngb to form the product complex.     

Coordination of diatomic ligands to heme: simply CO

The synthesis and molecular structures of three iron(II) porphyrinates with only CO as the axial ligand(s) are reported. Two five-coordinate [Fe(OEP)(CO)] derivatives have Fe-C = 1.7077(13) and 1.7140(10) A, much shorter than those of six-coordinate [Fe(OEP)(Im)(CO)], although nu(C-O) is 1944-1948 cm(-1). The six-coordinate species [Fe(OEP)(CO)2] has also been studied. The competition for pi-back-bonding of two CO ligands leads to Fe-C distance of 1.8558(10) A and nu(C-O) being increased to 2021 cm(-1). The M?ssbauer spectrum has a quadrupole splitting constant of 0 mm/s at 4.2 K, indicating high electronic symmetry.     

Role of heme propionates of myoglobin in vibrational energy relaxation

The role of heme propionates of myoglobin in vibrational energy relaxation was studied by time-resolved resonance Raman spectroscopy. Time-resolved anti-Stokes spectra were measured to monitor the vibrational energy relaxation of the heme. The decay rates of the band intensities were compared between wild-type myoglobin and etioheme-substituted myoglobin where the heme lacks hydrogen-bonding side chains. The decay rates of the anti-Stokes intensities of the latter were less than those of the former, providing strong support for a theoretical proposal that the propionates and their coupling to solvent bath play an important role in the dissipation of excess energy of the excited heme in solvated wild-type myoglobin.     

Inclusion chemistry for the modeling of heme proteins

Early attention to the modeling of heme proteins is enhancing the understanding of biochemistry. Those studies are also contributing to the development of techniques for the modeling of still more intricate, multifunctional, variously selective natural systems. Selectivity in simple systems may involve the molecular capability to bind only one of a family of related species or it may mean the ability to select and control one of a number of possible functions of a given bound species. Complicated systems simultaneously combine the two kinds of simple selectivities for two or more different classes of guest, often with synergistic interrelationships. The subject is developed around examples of binary, tertiary, and quarternary complexes designed to model the behavior of monooxygenases.     

On spectral relaxation in proteins

During the past several years there has been debate about the origins of nonexponential intensity decays of intrinsic tryptophan (trp) fluorescence of proteins, especially for single tryptophan proteins (STP). In this review we summarize the data from diverse sources suggesting that time-dependent spectral relaxation is a ubiquitous feature of protein fluorescence. For most proteins, the observations from numerous laboratories have shown that for trp residues in proteins (1) the mean decay times increase with increasing observation wavelength; (2) decay associated spectra generally show longer decay times for the longer wavelength components; and (3) collisional quenching of proteins usually results in emission spectral shifts to shorter wavelengths. Additional evidence for spectral relaxation comes from the time-resolved emission spectra that usually shows time-dependent shifts to longer wavelengths. These overall observations are consistent with spectral relaxation in proteins occurring on a subnanosecond timescale. These results suggest that spectral relaxation is a significant if not dominant source of nonexponential decay in STP, and should be considered in any interpretation of nonexponential decay of intrinsic protein fluorescence.     

Non-exponential phosphorescence decay of phenanthrene in biphenyl

Non-exponential phosphorescence decays of phenanthrene in biphenyl polycrystals have been observed. It is found that excitation with short duration quickens the decay while the decay is slower after excitation with weaker intensity. The origin of the non-exponentiality is ascribed to the distance-dependent interactions between guest molecules in the lowest excited triplet state.     

Extrapolation of accelerated thermooxidative tests to lower temperatures applying non-Arrhenius temperature functions

Extrapolations of the accelerated thermooxidative tests, based on the Arrhenius and two non-Arrhenius temperature functions, have been tested for 26 data sets. The data cover a wide range of materials from polyolefins and other polymers to biodiesel, edible oils and dried milk. It has been found that the extrapolation from high-temperature data to ambient temperature based on the Arrhenius temperature function leads to the estimations of unrealistically long durability. The best estimations corresponding most with experience are obtained for the extrapolation based on the temperature function k(T)=A _kexp(DT).     

13C NMR spectroscopy of core heme carbons as a simple tool to elucidate the coordination state of ferric high-spin heme proteins

Evidence is presented demonstrating that the magnitudes of the 13C chemical shifts originating from heme meso carbons provide a straightforward diagnostic tool to elucidate the coordination state of high-spin heme proteins and enzymes. Pentacoordinate high-spin heme centers exhibit 13C meso shifts centered at approximately 250 ppm, whereas their hexacoordinate counterparts exhibit 13C shifts centered at approximately -80 ppm. The relatively small spectral window (400 to -100 ppm) covering the meso-13C shifts, the relatively narrow lines of these resonances, and the availability of biosynthetic methods to prepare 13C-labeled heme (Rivera, M.; Walker, F. A. Anal. Biochem. 1995, 230, 295-302) make this approach practical. The theoretical basis for the distinct chemical shifts observed for meso carbons from hexacoordinate high-spin hemes relative to their pentacoordinate counterparts are now well understood (Cheng, R.-J.; Chen, P. Y.; Lovell, T.; Liu, T.; Noodleman, L.; Case, D. A. J. Am. Chem. Soc. 2003, 125, 6774-6783), which indicates that the magnitude of the meso-carbon chemical shifts can be used as a simple and reliable diagnostic tool for determining the coordination state of the heme active sites, independent of the nature of the proximal ligand. Proof of the principle for the 13C NMR spectroscopic approach is demonstrated using hexa- and pentacoordinate myoglobin. Subsequently, 13C NMR spectroscopy has been used to unambiguously determine that a recently discovered heme protein from Shigella dysenteriae (ShuT) is pentacoordinate.     

Electron transfer of heme proteins on the ITO electrode in polymer solvents

The redox reaction of poly(ethylene oxide) (PEO)-modified hemoglobin (PEO–Hb) was analyzed in PEO oligomers with cyclic voltammetry. The PEO–Hb was made soluble in PEO with molecular weight of 200 (PEO₂₀₀) containing 0.5 M KCI. Quasi-reversible redox signals of PEO–Hb were obtained by using an indium tin oxide (ITO) glass working electrode. PEO–Hb, cast on the ITO electrode, also showed the redox response in PEO with molecular weight of 400 (PEO₄₀₀). The peak current of PEO–Hb on the ITO electrode gradually increased during potential cycling. The effect of the scan rate on the quantity of electricity (Q) was analyzed after the peak current reached a constant value. The constant Q value was observed at the scan rate ranging from 30 to 500 mV/sec. The number of reactive PEO–Hb molecules was estimated from this constant Q-value. It was suggested that the electron transfer was carried out at the first layer of the PEO–Hb which was in direct contact with the ITO electrode. The quantity of electricity of PEO–Hb increased when the ITO electrode was first washed in an aqueous medium with ultrasonicator. This strongly suggested that the more effective surface area of the ITO electrode turned to be covered with PEO–Hb when the microporous region of the ITO particles was more hydrated.     

Reactions of heme proteins with carbonate radical anion

Reactions of radiolytically generated CO₃ ^•− with some ferric heme proteins, catalase, cytochrome c, and horseradish peroxidase (HRP), were studied. Carbonate radical anion oxidized amino acid residues of these proteins, but did not react directly with heme iron. HRP and catalase lost about 30% and 20% of their activity, respectively, after the reaction with 100 μM of CO₃ ^•−. The rate constants of the reactions of CO₃ ^•− with the investigated proteins measured by the pulse radiolysis method at pH 8–8.4 and 10 varied from 1.0 × 10⁸ M⁻¹ s⁻¹ (for cytochrome c) to 3.7 × 10⁹ M⁻¹ s⁻¹ (for catalase).