How O2 binds to heme: reasons for rapid binding and spin inversion

We have used density functional methods to calculate fully relaxed potential energy curves of the seven lowest electronic states during the binding of O(2) to a realistic model of ferrous deoxyheme. Beyond a Fe-O distance of approximately 2.5 A, we find a broad crossing region with five electronic states within 15 kJ/mol. The almost parallel surfaces strongly facilitate spin inversion, which is necessary in the reaction of O(2) with heme (deoxyheme is a quintet and O(2) a triplet, whereas oxyheme is a singlet). Thus, despite a small spin-orbit coupling in heme, the transition probability approaches unity. Using reasonable parameters, we estimate a transition probability of 0.06-1, which is at least 15 times larger than for the nonbiological Fe-O(+) system. Spin crossing is anticipated between the singlet ground state of bound oxyheme, the triplet and septet dissociation states, and a quintet intermediate state. The fact that the quintet state is close in energy to the dissociation couple is of biological importance, because it explains how both spin states of O(2) may bind to heme, thereby increasing the overall efficiency of oxygen binding. The activation barrier is estimated to be <15 kJ/mol based on our results and M?ssbauer experiments. Our results indicate that both the activation energy and the spin-transition probability are tuned by the porphyrin as well as by the choice of the proximal heme ligand, which is a histidine in the globins. Together, they may accelerate O(2) binding to iron by approximately 10(11) compared with the Fe-O(+) system. A similar near degeneracy between spin states is observed in a ferric deoxyheme model with the histidine ligand hydrogen bonded to a carboxylate group, i.e. a model of heme peroxidases, which bind H(2)O(2) in this oxidation state.     

Spin-orbit splitting for inner-shell 2p states

A strategy to calculate spin-orbit splitting for inner-shell transitions at an ab initio level is presented. The initial wave function is calculated for a spinless Hamiltonian at a multiconfigurational level, with just a few configurations, followed by multireference configuration interaction in order to establish a set of singlet and triplet states at 2p excitation edge. Then, the full Breit-Pauli Hamiltonian is formed and diagonalized on this state basis. The spin-orbit splitting is determined by a graphical procedure depending on the intensity of the transition from ground state. The specific states studied are those originating from 2p transitions in argon, HCl, H₂S, and PH₃.     

Electronic structure of boron-doped finite graphene sheets: unrestricted DFT and complete active space calculations

B3LYP and complete active space methods were applied to study graphene nanoribbons (GNRs) doped with boron atoms. The restricted B3LYP solutions were found to be unstable in all but two cases, and the complete active space calculations prove the multiconfigurational character of the ground state contributing with two most important configurations. The exception is the structure c4 where the system has single reference ground state in spite of the instability of the restricted wavefunction.

The distance between dopant atoms, their mutual position and their location within the nanoribbon impact the relative stability of doped nanoribbons. B doping does not modify the ionisation potentials of doped GNRs. However, it notably increases the electron affinity of the core-doped nanoribbons. The doping also has a notable impact on the reorganisation energy of the nanoribbons. The reorganisation energy of B-doped GNRs is higher than the corresponding reorganisation energy of pristine and nitrogen-doped GNRs.     

Two-dimensional boron nitride structures functionalization: first principles studies

Density functional theory calculations have been performed to investigate two-dimensional hexagonal boron nitride (2D hBN) structures functionalization with organic molecules. 2x2, 4x4 and 6x6 periodic 2D hBN layers have been considered to interact with acetylene. To deal with the exchange-correlation energy the generalized gradient approximation (GGA) is invoked. The electron-ion interaction is treated with the pseudopotential method. The GGA with the Perdew-Burke-Ernzerhoff (PBE) functionals together with van der Waals interactions are considered to deal with the composed systems. To investigate the functionalization two main configurations have been explored; in one case the molecule interacts with the boron atom and in the other with the nitrogen atom. Results of the adsorption energies indicate chemisorption in both cases. The total density of states (DOS) displays an energy gap in both cases. The projected DOS indicate that the B-p and N-p orbitals are those that make the most important contribution in the valence band and the H-s and C-p orbitals provide an important contribution in the conduction band to the DOS. Provided that the interactions of the acetylene with the 2D layer modify the structural and electronic properties of the hBN the possibility of structural functionalization using organic molecules may be concluded.     

Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor

The phosphodiesterase A1 protein of Acetobacter xylinum, AxPDEA1, is a key regulator of bacterial cellulose synthesis. This phosphodiesterase linearizes cyclic bis(3'-->5')diguanylic acid, an allosteric activator of the bacterial cellulose synthase, to the ineffectual pGpG. Here we show that AxPDEA1 contains heme and is regulated by reversible binding of O(2) to the heme. Apo-AxPDEA1 has less than 2% of the phosphodiesterase activity of holo-AxPDEA1, and reconstitution with hemin restores full activity. O(2) regulation is due to deoxyheme being a better activator than oxyheme. AxPDEA1 is homologous to the Escherichia coli direct oxygen sensor protein, EcDos, over its entire length and is homologous to the FixL histidine kinases over only a heme-binding PAS domain. The properties of the heme-binding domain of AxPDEA1 are significantly different from those of other O(2)-responsive heme-based sensors. The rate of AxPDEA1 autoxidation (half-life > 12 h) is the slowest observed so far for this type of heme protein fold. The O(2) affinity of AxPDEA1 (K(d) approximately 10 microM) is comparable to that of EcDos, but the rate constants for O(2) association (k(on) = 6.6 microM(-)(1) s(-)(1)) and dissociation (k(off) = 77 s(-)(1)) are 2000 times higher. Our results illustrate the versatility of signal transduction mechanisms for the heme-PAS class of O(2) sensors and provide the first example of O(2) regulation of a second messenger.     

Conformational substates of the oxyheme centers in alpha and beta subunits of hemoglobin as disclosed by EPR and ENDOR studies of cryoreduced protein

Exposure of frozen solutions of oxyhemoglobin to gamma-irradiation at 77 K yields EPR- and ENDOR-active, one-electron-reduced oxyheme centers which retain the conformation of the diamagnetic precursor. EPR spectra have been collected for the centers produced in human HbO(2) and isolated alphaO(2) and betaO(2) chains, as well as alphaO(2)beta(Zn), alpha(Zn)betaO(2), and alphaO(2)beta(Fe(3+)) hybrids, each in frozen buffer and in frozen glasses that form in the presence of glycols and sugars and also in the presence of IHP. These reveal two spectroscopically distinct classes of such ferriheme centers (g(1) 相似文献   

Characteristics of the serological passage of Escherichia isolated from children and adults with acute intestinal infections

The serological picture of Escherichia (5,910 strains), isolated from 1,430 inpatients (486 adults and 944 children) with acute intestinal infections by means of new diagnostic preparations (Escherichia rapid agglutinating O- and H-systems), was studied. In 15% of the adults and 26-28% of the children no Escherichia were detected. The serological picture of Escherichia proved to comprise 143 O-groups and 334 serovars; about 50% of the strains belonged to 11 prevailing O-groups: O1, O2, O4, O6, O7, O8, O9, O16, O21, O75, O85. The serological picture in the adults was more variegated than that in the children: from most of the patients (77.2%) Escherichia were isolated as a mixture of 2-9 serovars. The isolation rate of Escherichia monocultures and the incidence of Escherichia belonging to different O-groups were the same in patients of different ages, with the exception of groups O4, O6, O26, O55 and O111 which were more frequent in young children.     

Hydroxylation of deoxyguanosine at the C-8 position by ascorbic acid and other reducing agents

The C-8 position of deoxyguanosine (dGuo) was hydroxylated by ascorbic acid in the presence of oxygen (O2) in 0.1 M phosphate buffer (pH 6.8) at 37 degrees C. Addition of hydrogen peroxide (H2O2) remarkably enhanced this hydroxylation. The Udenfriend system [ascorbic acid, FeII, ethylenediaminetetraacetic acid (EDTA) and O2] was also effective for hydroxylation of dGuo in high yield. Guanine residues in DNA were also hydroxylated by ascorbic acid. Other reducing agents, such as hydroxylamine, hydrazine, dihydroxymaleic acid, sodium bisulfite and acetol, were also effective for the hydroxylation reaction, as were metal-EDTA complexes (FeII-, SnII-, TiIII-, CuI-EDTA). An OH radical seemed to be involved in this hydroxylation reaction in most of the above hydroxylating systems, but another reaction mechanism may also be involved, particularly when dGuo is hydroxylated by ascorbic acid alone or ascorbic acid plus H2O2. The possible biological significance of the hydroxylation of guanine residues in DNA in relation to mutagenesis and carcinogenesis is discussed.     

Three-dimensional representation of the many-body quantum state

Using the trajectory conception of state, we give a simple demonstration that the quantum state of a many-body system may be expressed as a set of states in three-dimensional space, each associated with a different particle. It follows that the many-body wavefunction may be derived from a set of waves in 3-space. Entanglement is represented in the trajectory picture by the mutual dependence of the 3-states on the trajectory labels.     

Some possible structures of lanthanoid carbonyl compounds

The CNDO/2 quantum chemical method was used to determine the most probable configurations for the carbonyl compounds of lanthanoids with different coordination numbers. The most probable structures were linear for RECO and RE(CO)₂, trigonal-pyramidal for RE(CO)₃, tetragonal-pyramidal for RE(CO)₃, tetragonal-pyramidal for RE(CO)₄ and RE(CO)₅, and trigonal-prismatic for RE(CO)₆. The 5d orbitals of the rare earths play a significant role in the formation of chemical bonds in the carbonyl compounds of lanthonoids. There is a linear relationship between the CO stretching frequencies and the net charges on the central rare earth atoms.     

Oxygen binding and redox properties of the heme in soluble guanylate cyclase: implications for the mechanism of ligand discrimination

Soluble guanylate cyclase is an NO-sensing hemoprotein that serves as a NO receptor in NO-mediated signaling pathways. It has been believed that this enzyme displays no measurable affinity for O(2), thereby enabling the selective NO sensing in aerobic environments. Despite the physiological significance, the reactivity of the enzyme-heme for O(2) has not been examined in detail. In this paper we demonstrated that the high spin heme of the ferrous enzyme converted to a low spin oxyheme (Fe(2+)-O(2)) when frozen at 77 K in the presence of O(2). The ligation of O(2) was confirmed by EPR analyses using cobalt-substituted enzyme. The oxy form was produced also under solution conditions at -7 °C, with the extremely low affinity for O(2). The low O(2) affinity was not caused by a distal steric protein effect and by rupture of the Fe(2+)-proximal His bond as revealed by extended x-ray absorption fine structure. The midpoint potential of the enzyme-heme was +187 mV, which is the most positive among high spin protoheme-hemoproteins. This observation implies that the electron density of the ferrous heme iron is relatively low by comparison to those of other hemoproteins, presumably due to the weak Fe(2+)-proximal His bond. Based on our results, we propose that the weak Fe(2+)-proximal His bond is a key determinant for the low O(2) affinity of the heme moiety of soluble guanylate cyclase.     

Secondary structural analysis of the Na(+),K(+)-ATPase and its Na(+) (E(1)) and K(+) (E(2)) complexes by FTIR spectroscopy

The Na(+),K(+)-ATPase is an integral membrane protein which transports sodium and potassium cations against an electrochemical gradient. The transport of Na(+) and K(+) ions is presumably connected to an oscillation of the enzyme between the two conformational states, the E(1) (Na(+)) and the E(2) (K(+)) conformations. The E(1) and E(2) states have different affinities for ligand interaction. However, the determination of the secondary structure of this enzyme in its sodium and potassium forms has been the subject of much controversy. This study was designed to provide a quantitative analysis of the secondary structure of the Na(+),K(+)-ATPase in its sodium (E(1)) and potassium (E(2)) states in both H(2)O and D(2)O solutions at physiological pH, using Fourier transform infrared (FTIR) with its self-deconvolution and second derivative resolution enhancement methods, as well as curve-fitting procedures. Spectroscopic analysis showed that the secondary structure of the sodium salt of the Na(+),K(+)-ATPase in H(2)O solution contains alpha-helix 19.8+/-1%, beta-sheet 25.6+/-1%, turn 9.1+/-1%, and beta-anti 7.5+/-1%, whereas in D(2)O solution, the enzyme shows alpha-helix 16.8+/-1%, beta-sheet 24.5+/-1.5%, turn 10.9+/-1%, beta-anti 9.8+/-1%, and random coil 38.0+/-2%. Similarly, the potassium salt in H(2)O solution contains alpha-helix 16.6+/-1%, beta-sheet 26.4+/-1.5%, turn 8.9+/-1%, and beta-anti 8.1+/-1%, while in D(2)O solution it shows alpha-helix 16.2+/-1%, beta-sheet 24.5+/-1.5%, turn 10.3+/-1%, beta-anti 9.0+/-1%, and random coil 40+/-2%. Thus the main differences for the sodium and potassium forms of the Na(+),K(+)-ATPase are alpha-helix 3.2% in H(2)O and 0.6% in D(2)O, beta-sheet (pleated and anti) 1.5% in H(2)O and random structure 2% (D(2)O), while for other minor components (turn structure), the differences are less than 1%.     

Electronic structure of DNA by DV-X alpha cluster calculations. I. d(GG).d(CC), d(CG)2, d(GC)2 A and B conformations

The electronic structure of d(GG).d(CC), d(CG)2, d(GC)2 which are stacked base pairs in the DNA double helix, are elucidated for both A and B conformations in detail by DV-X alpha cluster calculations. These three DNA double helix fragments are constructed from the same bases, G and C, but the electronic structure of the fragments for A and B conformations differs from each other characteristically. In particular, the electronic states of the O2 and O3 in phosphates differ drastically from each other, and might play a crucial role as recognition sites in various reaction processes concerning DNA. These differences are caused by the delicate differences in the admixture of the orbital components and the intra- and inter-bases interactions. Contour maps of the wavefunction of the HOMO and LUMO are compared among the stacking isomers.     

Benign posttraumatic encephalopathy

Twenty-eight post-injury states were assessed in 27 children (in one child two attacks occurred) aged 1-9 years. The states could be classed as so called benign posttraumatic encephalopathy. The mild head injury was followed after a latent period (proved in 22 attacks) of 5 min. to 14 hours by transient brain disorder (in 17 cases quantitative, qualitative and combined alteration in consciousness, in 7 children cortical blindness, in 2 epileptic seizure and in two brain stem disturbance). The duration of symptoms lasted 5 minutes to 48 hours. After recovery the children had no difficulties; the mean of follow-up was 3.3 years. The EEG showed predominantly a normal picture or only abnormal background activity of bioccipital slow waves. In the history and clinical picture we found after the attack most often perinatal abnormality and minimal brain dysfunction (15x, 57%) and various forms of migraine (4x, 16%). It indicates that in the pathogenesis of benign posttraumatic encephalopathy apparently an important part is played by pretraumatic cerebral affection.     

Phospholipids chiral at phosphorus. Stereochemical mechanism for the formation of inositol 1-phosphate catalyzed by phosphatidylinositol-specific phospholipase C.

The phosphatidylinositol-specific phospholipase C (PI-PLC) from mammalian sources catalyzes the simultaneous formation of both inositol 1,2-cyclic phosphate (IcP) and inositol 1-phosphate (IP). It has not been established whether the two products are formed in sequential or parallel reactions, even though the latter has been favored in previous reports. This problem was investigated by using a stereochemical approach. Diastereomers of 1,2-dipalmitoyl-sn-glycero-3-(1D- [16O,17O]phosphoinositol) ([16O,17O]DPPI) and 1,2-dipalmitoyl-sn-glycero-3-(1D-thiophosphoinositol) (DPPsI) were synthesized, the latter with known configuration. Desulfurization of the DPPsI isomers of known configurations in H2(18)O gave [16O,18O]DPPI with known configurations, which allowed assignment of the configurations of [16O,17O]DPPI on the basis of 31P NMR analyses of silylated [16O,18O]DPPI and [16O,17O]DPPI (the inositol moiety was fully protected in this operation). (Rp)- and (Sp)-[16O,17O]DPPI were then converted into trans- and cis-[16O,17O]IcP, respectively, by PI-PLC from Bacillus cereus, which had been shown to proceed with inversion of configuration at phosphorus [Lin, G., Bennett, F. C., & Tsai, M.-D. (1990) Biochemistry 29, 2747-2757]. 31P NMR analysis was again used to differentiate the silylated products of the two isomers of IcP, which then permitted assignments of IcP with unknown configuration derived from transesterification of (Rp)- and (Sp)-[16O,17O]DPPI by bovine brain PI-PLC-beta 1. The results indicated inversion of configuration, in agreement with the steric course of the same reaction catalyzed by PI-PLCs from B. cereus and guinea pig uterus reported previously. For the steric course of the formation of inositol 1-phosphate catalyzed by PI-PLC, (Rp)- and (Sp)-[16O,17O]DPPI were hydrolyzed in H2(18)O to afford 1-[16O,17O,18O]IP, which was then converted to IcP chemically and analyzed by 31P NMR. The results indicated that both B. cereus PI-PLC and the PI-PLC-beta 1 from bovine brain catalyze conversion of DPPI to IP with overall retention of configuration at phosphorus. These results suggest that both bacterial and mammalian PI-PLCs catalyze the formation of IcP and IP by a sequential mechanism. However, the conversion of IcP to IP was detectable by 31P NMR only for the bacterial enzyme. Thus an alternative mechanism in which IcP and IP are formed by totally independent pathways, with formation of IP involving a covalent enzyme-phosphoinositol intermediate, cannot be ruled out for the mammalian enzyme. It was also found that both PI-PLCs displayed lack of stereo-specifically toward the 1,2-diacylglycerol moiety, which suggests that the hydrophobic part of phosphatidylinositol is not recognized by PI-PLC.     

Effects of elevated atmospheric CO2 and/or O3 on intra- and interspecific competitive ability of aspen

Three model communities of trembling aspen (monoculture, and mixed with either paper birch or sugar maple) were grown for seven years in elevated atmospheric CO(2) and O(3) using Free Air CO(2) Enrichment (FACE) technology. We utilized trends in species' importance, calculated as an index of volume growth and survival, as indications of shifting community composition. For the pure aspen communities, different clones emerged as having the highest change in relative importance values depending on the pollutant exposure. In the control and elevated CO(2) treatments, clone 42E was rapidly becoming the most successful clone while under elevated O(3), clone 8 L emerged as the dominant clone. In fact, growth of clone 8 L was greater in the elevated O(3) treatment compared to controls. For the mixed aspen-birch community, importance of aspen and birch changed by - 16 % and + 62 %, respectively, in the controls. In the treatments, however, importance of aspen and birch changed by - 27 % and + 87 %, respectively, in elevated O(3), and by - 10 % and + 45 %, respectively, in elevated CO(2). Thus, the presence of elevated O(3) hastened conversion of stands to paper birch, whereas the presence of elevated CO(2) delayed it. Relative importance of aspen and maple changed by - 2 % and + 3 %, respectively, after seven years in the control treatments. But in elevated O(3), relative importance of aspen and maple changed by - 2 % and + 5 %, respectively, and in elevated CO(2) by + 9 and - 20 %, respectively. Thus, elevated O(3) slightly increases the rate of conversion of aspen stands to sugar maple, but maple is placed at a competitive disadvantage to aspen under elevated CO(2).     

The axial ligand effect of oxo-iron porphyrin catalysts. How does chloride compare to thiolate?

We have performed density functional theory calculations on an oxo-iron porphyrin catalyst with chloride as an axial ligand and tested its reactivity toward propene. The reactions proceed via multistate reactivity on competing doublet and quartet spin surfaces. Close-lying epoxidation and hydroxylation mechanisms are identified, whereby in the gas phase the epoxidation reaction is dominant, while in environments with a large dielectric constant the hydroxylation pathways become competitive. By contrast to reactions with thiolate as an axial ligand all low-lying pathways have small ring-closure and rebound barriers, so it is expected that side products and rearrangements will be unlikely with Fe=O(porphyrin)Cl, whereas with Fe=O(porphyrin)SH some side products were predicted. The major differences in the electronic configurations of Fe=O(porphyrin)Cl and Fe=O(porphyrin)SH are due to strong mixing of thiolate orbitals with iron 3d orbitals, a mixing which is much less with chloride as an axial ligand. Predictions of the reactivity of ethylbenzene-h ₁₂ versus ethylbenzene-d ₁₂ are made. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

On the role of the axial ligand in heme proteins: a theoretical study

We present a systematic investigation of how the axial ligand in heme proteins influences the geometry, electronic structure, and spin states of the active site, and the energies of the reaction cycles. Using the density functional B3LYP method and medium-sized basis sets, we have compared models with His, His+Asp, Cys, Tyr, and Tyr+Arg as found in myoglobin and hemoglobin, peroxidases, cytochrome P450, and heme catalases, respectively. We have studied 12 reactants and intermediates of the reaction cycles of these enzymes, including complexes with H(2)O, OH(-), O(2-), CH(3)OH, O(2), H(2)O(2), and HO(2)(-) in various formal oxidation states of the iron ion (II to V). The results show that His gives ~0.6 V higher reduction potentials than the other ligands. In particular, it is harder to reduce and protonate the O(2) complex with His than with the other ligands, in accordance with the O(2) carrier function of globins and the oxidative chemistry of the other proteins. For most properties, the trend Cys相似文献