Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin

Myoglobin (Mb) is perhaps the most studied protein, experimentally and theoretically. Despite the wealth of known details regarding the gas migration processes inside Mb, there exists no fully conclusive picture of these pathways. We address this deficiency by presenting a complete map of all the gas migration pathways inside Mb for small gas ligands (O2, NO, CO, and Xe). To accomplish this, we introduce a computational approach for studying gas migration, which we call implicit ligand sampling. Rather than simulating actual gas migration events, we infer the location of gas migration pathways based on a free-energy perturbation approach applied to simulations of Mb's dynamical fluctuations at equilibrium in the absence of ligand. The method provides complete three-dimensional maps of the potential of mean force of gas ligand placement anywhere inside a protein-solvent system. From such free-energy maps we identify each gas docking site, the pathways between these sites, to the heme and to the external solution. Our maps match previously known features of these pathways in Mb, but also point to the existence of additional exits from the protein matrix in regions that are not easily probed by experiment. We also compare the pathway maps of Mb for different gas ligands and for different animal species.     

Myoglobin discriminates between O2, NO, and CO by electrostatic interactions with the bound ligand

 Most biological substrates have distinctive sizes, shapes, and charge distributions which can be recognized specifically by proteins. In contrast, myoglobin must discriminate between the diatomic gases O₂, CO, and NO which are apolar and virtually the same size. Selectivity occurs at the level of the covalent Fe-ligand complexes, which exhibit markedly different bond strengths and electrostatic properties. By pulling a water molecule into the distal pocket, His64(E7)¹ inhibits the binding of all three ligands by a factor of ∼10 compared to that observed for protoheme-imidazole complexes in organic solvents. In the case of O₂ binding, this unfavorable effect is overcome by the formation of a strong hydrogen bond between His64(E7) and the highly polar FeO₂ complex. This favorable electrostatic interaction stabilizes the bound O₂ by a factor of ∼1000, and the net result is a 100-fold increase in overall affinity compared to model hemes or mutants with an apolar residue at position 64. Electrostatic interaction between FeCO and His64 is very weak, resulting in only a two- to three-fold stabilization of the bound state. In this case, the inhibitory effect of distal pocket water dominates, and a net fivefold reduction in K _CO is observed for the wild-type protein compared to mutants with an apolar residue at position 64. Bound NO is stabilized ∼tenfold by hydrogen bonding to His64. This favorable interaction with FeNO exactly compensates for the tenfold inhibition due to the presence of distal pocket water, and the net result is little change in K _NO when the distal histidine is replaced with apolar residues. Thus, it is the polarity of His64 which allows discrimination between the diatomic gases. Direct steric hindrance by this residue plays a minor role as judged by: (1) the independence of K _O2, K _CO, and K _NO on the size of apolar residues inserted at position 64, and (2) the observation of small decreases, not increases, in CO affinity when the mobility of the His64 side chain is increased. Val68(E11) does appear to hinder selectively the binding of CO. However, the extent is no more than a factor of 2–5, and much smaller than electrostatic stabilization of bound O₂ by the distal histidine. Received, accepted: 23 May 1997     

Heme-linked protonation of HCN, CO, NO and O2 complexes of reduced horseradish peroxidases.

Small reversible changes in the absorption spectra of HCN, CO, NO and O₂ complexes of ferrous diacetyldeuteroperoxidase A, not hitherto observed, were attributed to proton dissociation of a distal amino acid residue. From spectrophotometric titration data the pK_a was measured as 5.5 (HCN), 5.6 (ligand free), 6.0 (CO), 6.55 (NO) and 8.0 (O₂). The value of 8.0 for the pK_a of the O₂ complex was also obtained from a curve of pH dependence of proton uptake in the reaction of the ferrous enzyme with O₂. Absorption bands in the visible region were shifted to longer wavelengths in the order of CO to NO to O₂ which is the decreasing order of the energy of π¹ level of these diatomic ligands.The pK_a values for CO complexes of ferroperoxidases, isoenzymes A and (B+C) were varied with substituents at the 2 and 4 positions of deuterohemin IX, and the $\text{Δp}\text{K}{}_{\mathrm{<mtext>a</mtext>}}\text{Δp}\text{K}{}_3$ ratio was about 0.3 in both series of isoenzyme preparations, where pK₃ is a measure of basicity of pyrrole nitrogen.The present data support the previous conclusion (Yamada and Yamazaki (1974) Arch. Biochem. Biophys., 165, 728) that the pK_a for ferroperoxidases, measured from small reversible changes in the absorption spectra, represents a proton dissociation constant of a distal amino acid residue and that there is hydrogen bonding between the residue and a ligand atom directly bound to the iron atom.     

Diffusing capacity reexamined: relative roles of diffusion and chemical reaction in red cell uptake of O2, CO, CO2, and NO.

This paper presents an analytical expression for the diffusing capacity (Theta(t)) of the red blood cell (RBC) for any reactive gas in terms of size and shape of the RBC, thickness of the unstirred plasma layer surrounding the RBC, diffusivities and solubilities of the gas in RBC and boundary layer, hematocrit, and the slope of the dissociation curve. The expression for Theta(t) has been derived by spatial averaging of the fundamental convection-diffusion-reaction equation for O(2) in the RBC and has been generalized to all cell shapes and for other reactive gases such as CO, NO, and CO(2). The effects of size and shape of the RBC, thickness of the unstirred plasma layer, hemoglobin concentration, and hematocrit on Theta(t) have been analyzed, and the analytically obtained expression for Theta(t) has been validated by comparison with different sets of existing experimental data for O(2) and CO(2). Our results indicate that the discoidal shape of the human RBC with average dimensions of 1.6-mum thickness and 8-mum diameter is close to optimal design for O(2) uptake and that the true reaction velocity in the RBC is suppressed significantly by the mass transfer resistance in the surrounding unstirred layer. In vitro measurements using rapid-mixing technique, which measures Theta(t) in the presence of artificially created large boundary layers, substantially underpredicts the in vivo diffusing capacity of the RBC in the diffusion-controlled regime. Depending on the conditions in the RBC, uptake of less reactive gases (such as CO) undergoes transition from reaction-limited to diffusion-limited regime. For a constant set of morphological parameters, the theoretical expression for Theta(t) predicts that Theta(t,NO) > Theta(t,)(CO(2)) > Theta(t,)(O(2)) > Theta(t,CO).     

Reactions of PTIO and carboxy-PTIO with *NO, *NO2, and O2-*

Nitronyl nitroxides, such as derivatives of 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl 3-oxide (PTIOs), react with *NO to form the corresponding imino nitroxides (PTIs) and *NO2. PTIOs are considered as monitors of *NO, stoichiometric sources of *NO2, biochemical and physiological effectors, specific tools for the elimination of *NO, and potential therapeutic agents. However, a better understanding of the chemical properties of PTIOs, especially following their reaction with *NO, is necessary to resolve many of the reported discrepancies surrounding the effects of PTIOs and to better characterize their potential therapeutic activity. We have generated electrochemically the oxidized and reduced forms of PTIO and carboxy-PTIO (C-PTIO), characterized their absorption spectra, and determined the reduction potentials for the oxoammonium/nitroxide and nitroxide/hydroxylamine couples. The rate constants for the reaction of *NO2 with PTIO and C-PTIO to form the corresponding oxoammonium cations (PTIO+s) and nitrite were determined to be (1.5 - 2) x 10(7) m-1 s-1. We have also shown that the reactions of PTIO+s with *NO form PTIOs and NO2-. The rate constants for these reactions are approximately 30-fold higher than those for the reactions of PTIOs with *NO or O2-*. The present results show that (i) the reaction of PTIOs with *NO forms solely PTIs and NO2- where [NO2-]/[PTI] varies between 1 and 2 depending on the steady-state concentrations of *NO. Consequently, quantitation of *NO is valid only at sufficiently low fluxes of *NO; (ii) the reaction of PTIOs with *NO can be used as a valid source of *NO2 only when the latter is effectively scavenged by an appropriate reductant; and (iii) the formation of peroxynitrite cannot be efficiently inhibited by PTIOs even under relatively low fluxes of *NO and O2-* and millimolar levels of PTIOs.     

Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO).

Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.     

Influence of carbon availability on the production of NO, N2O, N2 and CO2 by soil cores during anaerobic incubation

Net productions of permanent soil atmosphere gases (N₂, CO₂, O₂) and temporary gases (N₂O, NO) were monitored in soil cores using a non-interfering, fully automated measuring technique allowing highly time resolved measurements over prolonged periods. The influence of changes in available organic carbon on CO₂, N₂O, NO and N₂ production was studied by changing the soil carbon content through aerobic preincubations of different length, up to 21 days.The aerobic preincubation caused an increase in NO₃ ^- concentration and a decrease in available carbon content. Available carbon content dominated both CO₂ and total N gas (N₂+N₂O+NO) production during anaerobiosis. Both CO₂ and total N gas production rates decreased with increasing length of the previous aerobic preincubation, this in spite of the higher initial NO₃ ^- concentration.Total denitrification rates were closely related to the anaerobic CO₂ production rates. No relation was found between water soluble carbon content and total denitrification. The N₂O/N₂ ratio could be explained by an interaction of carbon availability, NO₃ ^- concentration and enzyme status. Net N₂O consumption was monitored. The balance between cumulative total N gas production and NO₃ ^- consumption varied according to the different treatments. Cumulative N₂O production exceeded cumulative N₂ production for 0 up to 5 days.     

Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO2(-) and O2 concentrations.

The oxygen control of denitrification and its emission of NO/N2O/N2 was investigated by incubation of Nycodenz-extracted soil bacteria in an incubation robot which monitors O2, NO, N2O and N2 concentrations (in He+O2 atmosphere). Two consecutive incubations were undertaken to determine (1) the regulation of denitrification by O2 and NO2(-) during respiratory O2 depletion and (2) the effects of re-exposure to O2 of cultures with fully expressed denitrification proteome. Early denitrification was only detected (as NO and N2O) at 相似文献   

Heterotrophic nitrification by Alcaligenes faecalis: NO2-, NO3-, N2O, and NO production in exponentially growing cultures

Heterotrophic nitrification by Alcaligenes faecalis DSM 30030 was not restricted to media containing organic forms of nitrogen. In both peptone-meat extract and defined media with ammonium and citrate as the sole nitrogen and carbon sources, respectively, NO2-, NO3-, NO, and N2O were produced under aerobic growth conditions. Heterotrophic nitrification was not attributable to old or dying cell populations. Production of NO2-, NO3-, NO, and N2O was detectable shortly after cultures started growth and proceeded exponentially during the logarithmic growth phase. NO2- and NO3- production rates were higher for cultures inoculated in media with pH values below 7 than for those in media at alkaline pH. Neither assimilatory nor dissimilatory nitrate or nitrite reductase activities were detectable in aerobic cultures.     

The Impact of Nitrogen Placement and Tillage on NO, N2O, CH4 and CO2 Fluxes from a Clay Loam Soil

To evaluate the impact of N placement depth and no-till (NT) practice on the emissions of NO, N₂O, CH₄ and CO₂ from soils, we conducted two N placement experiments in a long-term tillage experiment site in northeastern Colorado in 2004. Trace gas flux measurements were made 2–3 times per week, in zero-N fertilizer plots that were cropped continuously to corn (Zea mays L.) under conventional-till (CT) and NT. Three N placement depths, replicated four times (5, 10 and 15 cm in Exp. 1 and 0, 5 and 10 cm in Exp. 2, respectively) were used. Liquid urea–ammonium nitrate (UAN, 224 kg N ha⁻¹) was injected to the desired depth in the CT- or NT-soils in each experiment. Mean flux rates of NO, N₂O, CH₄ and CO₂ ranged from 3.9 to 5.2 μg N m⁻² h⁻¹, 60.5 to 92.4 μg N m⁻² h⁻¹, −0.8 to 0.5 μg C m⁻² h⁻¹, and 42.1 to 81.7 mg C m⁻² h⁻¹ in both experiments, respectively. Deep N placement (10 and 15 cm) resulted in lower NO and N₂O emissions compared with shallow N placement (0 and 5 cm) while CH₄ and CO₂ emissions were not affected by N placement in either experiment. Compared with N placement at 5 cm, for instance, averaged N₂O emissions from N placement at 10 cm were reduced by more than 50% in both experiments. Generally, NT decreased NO emission and CH₄ oxidation but increased N₂O emissions compared with CT irrespective of N placement depths. Total net global warming potential (GWP) for N₂O, CH₄ and CO₂ was reduced by deep N placement only in Exp. 1 but was increased by NT in both experiments. The study results suggest that deep N placement (e.g., 10 cm) will be an effective option for reducing N oxide emissions and GWP from both fertilized CT- and NT-soils.     

Heterotrophic nitrification by Alcaligenes faecalis: NO2-, NO3-, N2O, and NO production in exponentially growing cultures.

Heterotrophic nitrification by Alcaligenes faecalis DSM 30030 was not restricted to media containing organic forms of nitrogen. In both peptone-meat extract and defined media with ammonium and citrate as the sole nitrogen and carbon sources, respectively, NO2-, NO3-, NO, and N2O were produced under aerobic growth conditions. Heterotrophic nitrification was not attributable to old or dying cell populations. Production of NO2-, NO3-, NO, and N2O was detectable shortly after cultures started growth and proceeded exponentially during the logarithmic growth phase. NO2- and NO3- production rates were higher for cultures inoculated in media with pH values below 7 than for those in media at alkaline pH. Neither assimilatory nor dissimilatory nitrate or nitrite reductase activities were detectable in aerobic cultures.     

A theoretical study on the binding of O(2), NO and CO to heme proteins

The hybrid density functional B3LYP is used to describe the bonding of the diatomic molecules O(2), NO and CO to ferrous heme. Three different models are used, a five-coordinated porphyrin in benzene, the myoglobin active site including the distal histidine and the binuclear center in cytochrome oxidase. The geometric and electronic structures are well described by the B3LYP functional, while experimental binding energies are more difficult to reproduce. It is found that the Cu(B) center in cytochrome oxidase has a similar effect on the binding of the diatomics as the distal histidine in myoglobin.     

Robotized incubation system for monitoring gases (O2, NO, N2O N2) in denitrifying cultures

As genomic data for bacteria are unraveled at an increasing speed, there is a need for more efficient and refined techniques to characterize metabolic traits. The regulatory apparatus for denitrification, for instance, has been explored extensively for type strains, but we lack refined observations of how these and wild type denitrifiers respond metabolically to changing environmental conditions. There is a need for new "phenomic" approaches, and the present paper describes one; an automated incubation system for the study of gas kinetics in 15 parallel bacterial cultures. An autosampler with a peristaltic pump takes samples from the headspace, and replaces the sampled gas with He by reversing the pump. The sample flows through the injector of a micro GC (for determination of N(2), O(2), CH(4), CO(2), N(2)O) to the inlet of a chemoluminescence NO analyzer. The linear range for NO is 0.5-10(4) ppmv (CV=2%, detection limit 0.2 ppmv). The gas leakage of N(2) into the system is low and reproducible, allowing the quantification of N(2) production (in flasks with He+O(2) atmosphere) with a detection limit of 150-200 nmol N(2) for a single time increment. The gas loss by each sampling is taken into account, securing mass balance for all gases, thus allowing accurate estimation of electron flows to the various terminal acceptors (O(2), NO(2)(-), NO, N(2)O) throughout the culture's depletion of O(2) and NO(x). We present some experimental results with Agrobacterium tumefaciens, Paracoccus denitrificans and denitrifying communities, demonstrating the system's potential for unraveling contrasting patterns of denitrification gene expression as a function of concentrations of O(2) and NO in the medium.     

Inhibitory and enhancing effects of NO on H2O2 toxicity: Dependence on the concentrations of NO and H2O2

Nitric oxide (NO) has been shown to both enhance hydrogen peroxide (H₂O₂) toxicity and protect cells against H₂O₂ toxicity. In order to resolve this apparent contradiction, we here studied the effects of NO on H₂O₂ toxicity in cultured liver endothelial cells over a wide range of NO and H₂O₂ concentrations. NO was generated by spermine NONOate (SpNO, 0.001–1 mM), H₂O₂ was generated continuously by glucose/glucose oxidase (GOD, 20–300 U/l), or added as a bolus (200 μM). SpNO concentrations between 0.01 and 0.1 mM provided protection against H₂O₂-induced cell death. SpNO concentrations >0.1 mM were injurious with low H₂O₂ concentrations, but protective at high H₂O₂ concentrations. Protection appeared to be mainly due to inhibition of lipid peroxidation, for which SpNO concentrations as low as 0.01 mM were sufficient. SpNO in high concentration (1 mM) consistently raised H₂O₂ steady-state levels in line with inhibition of H₂O₂ degradation. Thus, the overall effect of NO on H₂O₂ toxicity can be switched within the same cellular model, with protection being predominant at low NO and high H₂O₂ levels and enhancement being predominant with high NO and low H₂O₂ levels.     

H2O2 and (.)NO scavenging by Mycobacterium leprae truncated hemoglobin O

Kinetics of ferric Mycobacterium leprae truncated hemoglobin O (trHbOFe(III)) oxidation by H₂O₂ and of trHbOFe(IV)O reduction by NO and NO₂⁻ are reported. The value of the second-order rate constant for H₂O₂-mediated oxidation of trHbOFe(III) is 2.4 × 10³ M⁻¹ s⁻¹. The value of the second-order rate constant for NO-mediated reduction of trHbOFe(IV)O is 7.8 × 10⁶ M⁻¹ s⁻¹. The value of the first-order rate constant for trHbOFe(III)ONO decay to the resting form trHbOFe(III) is 2.1 × 10¹ s⁻¹. The value of the second-order rate constant for NO₂⁻-mediated reduction of trHbOFe(IV)O is 3.1 × 10³ M⁻¹ s⁻¹. As a whole, trHbOFe(IV)O, generated upon reaction with H₂O₂, catalyzes NO reduction to NO₂⁻. In turn, NO and NO₂⁻ act as antioxidants of trHbOFe(IV)O, which could be responsible for the oxidative damage of the mycobacterium. Therefore, Mycobacterium leprae trHbO could be involved in both H₂O₂ and NO scavenging, protecting from nitrosative and oxidative stress, and sustaining mycobacterial respiration.