Structural studies of constitutive nitric oxide synthases with diatomic ligands bound

Crystal structures are reported for the endothelial nitric oxide synthase (eNOS)–arginine–CO ternary complex as well as the neuronal nitric oxide synthase (nNOS) heme domain complexed with l-arginine and diatomic ligands, CO or NO, in the presence of the native cofactor, tetrahydrobiopterin, or its oxidized analogs, dihydrobiopterin and 4-aminobiopterin. The nature of the biopterin has no influence on the diatomic ligand binding. The binding geometries of diatomic ligands to nitric oxide synthase (NOS) follow the {MXY} ⁿ formalism developed from the inorganic diatomic–metal complexes. The structures reveal some subtle structural differences between eNOS and nNOS when CO is bound to the heme which correlate well with the differences in CO stretching frequencies observed by resonance Raman techniques. The detailed hydrogen-bonding geometries depicted in the active site of nNOS structures indicate that it is the ordered active-site water molecule rather than the substrate itself that would most likely serve as a direct proton donor to the diatomic ligands (CO, NO, as well as O₂) bound to the heme. This has important implications for the oxygen activation mechanism critical to NOS catalysis.     

Phosphorus acquisition and competitive abilities of two herbivorous zooplankton, <Emphasis Type="Italic">Daphnia pulex</Emphasis> and <Emphasis Type="Italic">Ceriodaphnia quadrangula</Emphasis>

Contrary to an expectation from the size-efficiency hypothesis, small herbivore zooplankton such as Ceriodaphnia often competitively predominate against large species such as Daphnia. However, little is known about critical feeding conditions favoring Ceriodaphnia over Daphnia. To elucidate these conditions, a series of growth experiments was performed with various types of foods in terms of phosphorus (P) contents and composition (algae and bacteria). An experiment with P-rich algae showed that the threshold food level, at which an individual’s growth rate equals zero, was not significantly different between the two species. However, the food P:C ratio, at which the growth rate becomes zero, was lower for Daphnia than for Ceriodaphnia, suggesting that the latter species is rather disfavored by P-poor algae. Ceriodaphnia showed a higher growth rate than Daphnia only when a substantial amount of bacteria was supplied together with a low amount of P-poor algae as food. These results suggest that an abundance of bacteria relative to algae plays a crucial role in favoring Ceriodaphnia over Daphnia because these are an important food resource for the former species but not for the latter.     

Seasonal succession of zooplankton in the north basin of Lake Biwa

To examine the seasonal succession of the entire zooplankton community in Lake Biwa, zooplankton biomass (on an areal basis) and its distribution patterns among crustaceans, rotifers and ciliates were studied in the north basin from April 1997 to June 1998. Seasonal changes in phytoplankton and population dynamics of Daphnia galeata were also examined to assess food condition and predation pressure by fish. From March to November, crustaceans dominated zooplankton biomass, but rotifers and ciliates were dominant from December to February. Among crustaceans, Eodiaptomus japonicus was the most abundant species, followed by D. galeata. Zooplankton biomass increased from January to a peak in early April, just before the spring bloom of phytoplankton, then decreased in mid-April when mortality rate of D. galeata increased. From mid-June, zooplankton increased and maintained a high level until the beginning of November. During this period, both birth and mortality rates of D. galeata were relatively high and a number of rotifer and crustacean species were observed. However, their abundances were very limited except for E. japonicus which likely preys on ciliates and rotifers. In Lake Biwa, food sources other than phytoplankton, such as resuspended organic matter from the sediments, seems to play a crucial role in zooplankton succession from winter to early spring, while zooplankton community seems to be regulated mainly by fish predation from summer to fall.     

The influence of fluctuating light intensities on species composition and diversity of natural phytoplankton communities

The influence of fluctuating light intensities on phytoplankton composition and diversity was investigated for 49 days under semi-continuous culture conditions with sufficient nutrient supply, using phytoplankton assemblages from Lake Biwa, Japan. Light conditions were either periodically changed from high intensity (100 µmol photons m^-2 s^-1) to low intensity (20 µmol photons m^-2 s^-1) at intervals of 1, 3, 6 and 12 days, or fixed to constant intensities (permanent high and low light levels). All treatments additionally experienced a day:night cycle of 16:8 h. Phytoplankton abundance increased and reached a saturation level on day 19 of the treatment with permanent high light, but increased continuously until the end of the experiment (day 49) in the treatment with permanent low light intensity. In treatments with periodically changing light intensities, the phytoplankton abundance reached saturation levels between these dates. Under phytoplankton abundance saturation, chlorophytes predominated in the treatment with permanent high light, while either cyanophytes or diatoms were abundant under permanent low light intensity. Treatments with changing light supply had chlorophyte- and cyanobacteria-dominated replicates as well as replicates with balanced proportions of both. Furthermore, species diversity, measured by the Shannon index, was low in cultures under permanent light intensity, while slow fluctuating light at the scale of 3 -12 days resulted in an increased diversity index. These results indicate that species composition and diversity of the phytoplankton were affected by the periodically changing light regime in the order of days, and suggest that temporal changes in weather conditions are a major impediment to competitive exclusion of phytoplankton species in nature.     

Elucidation of the heme binding site of heme-regulated eukaryotic initiation factor 2alpha kinase and the role of the regulatory motif in heme sensing by spectroscopic and catalytic studies of mutant proteins

Heme-regulated eukaryotic initiation factor 2alpha (eIF2alpha) kinase (HRI) functions in response to the heme iron concentration. At the appropriate heme iron concentrations under normal conditions, HRI function is suppressed by binding of the heme iron. Conversely, upon heme iron shortage, HRI autophosphorylates and subsequently phosphorylates the substrate, eIF2alpha, leading to the termination of protein synthesis. The molecular mechanism of heme sensing by HRI, including identification of the specific binding site, remains to be established. In the present study we demonstrate that His-119/His-120 and Cys-409 are the axial ligands for the Fe(III)-protoporphyrin IX complex (hemin) in HRI, based on spectral data on site-directed mutant proteins. Cys-409 is part of the heme-regulatory Cys-Pro motif in the kinase domain. A P410A full-length mutant protein displayed loss of heme iron affinity. Surprisingly, inhibitory effects of the heme iron on catalysis and changes in the heme dissociation rate constants in full-length His-119/His-120 and Cys-409 mutant proteins were marginally different to wild type. In contrast, heme-induced inhibition of Cys-409 mutants of the isolated kinase domain and N-terminal-truncated proteins was substantially weaker than that of the full-length enzyme. A pulldown assay disclosed heme-dependent interactions between the N-terminal and kinase domains. Accordingly, we propose that heme regulation is induced by interactions between heme and the catalytic domain in conjunction with global tertiary structural changes at the N-terminal domain that accompany heme coordination and not merely by coordination of the heme iron with amino acids on the protein surface.     

Binding of oxygen and carbon monoxide to a heme-regulated phosphodiesterase from Escherichia coli. Kinetics and infrared spectra of the full-length wild-type enzyme, isolated PAS domain, and Met-95 mutants

The heme-regulated phosphodiesterase, Ec DOS, is a redox sensor that uses the heme in its PAS domain to regulate catalysis. The rate of O(2) association (k(on)) with full-length Ec DOS is extremely slow at 0.0019 microM(-1) s(-1), compared with >9.5 microM(-1) s(-1) for 6-coordinated globin-type hemoproteins, as determined by the stopped-flow method. This rate is dramatically increased (up to 16-fold) in the isolated heme-bound PAS domain. Dissociation constants (K(d)) calculated from the kinetic parameters are 340 and 20 microm for the full-length wild-type enzyme and its isolated PAS domain, respectively. Mutations at Met-95 in the isolated PAS domain, which may be a heme axial ligand in the Fe(II) complex, lead to a further increase in the k(on) value by more than 30-fold, and consequently, a decrease in the K(d) value to less than 1 microM. The k(on) value for CO binding to the full-length wild-type enzyme is also very low (0.00081 microM(-1) s(-1)). The kinetics of CO binding to the isolated PAS domain and its mutants are similar to those observed for O(2). However, the K(d) values for CO are considerably lower than those for O(2).     

SOUL in mouse eyes is a new hexameric heme-binding protein with characteristic optical absorption, resonance Raman spectral, and heme-binding properties

SOUL is specifically expressed in the retina and pineal gland and displays more than 40% sequence homology with p22HBP, a heme protein ubiquitously expressed in numerous tissues. SOUL was purified as a dimer in the absence of heme from the Escherichia coli expression system but displayed a hexameric structure upon heme binding. Heme-bound SOUL displayed optical absorption and resonance Raman spectra typical of 6-coordinate low-spin heme protein, with one heme per monomeric unit for both the Fe(III) and Fe(II) complexes. Spectral data additionally suggest that one of the axial ligands of the Fe(III) heme complex is His. Mutation of His42 (the only His of SOUL) to Ala resulted in loss of heme binding, confirming that this residue is an axial ligand of SOUL. The K(d) value of heme for SOUL was estimated as 4.8 x 10(-9) M from the association and dissociation rate constants, suggesting high binding affinity. On the other hand, p22HBP was obtained as a monomer containing one heme per subunit, with a K(d) value of 2.1 x 10(-11) M. Spectra of heme-bound p22HBP were different from those of SOUL but similar to those of heme-bound bovine serum albumin in which heme bound to a hydrophobic cavity with no specific axial ligand coordination. Therefore, the heme-binding properties and coordination structure of SOUL are distinct from those of p22HBP, despite high sequence homology. The physiological role of the new heme-binding protein, SOUL, is further discussed in this report.     

Exploring the binding conformations of bulkier dipeptide amide inhibitors in constitutive nitric oxide synthases

A series of L-nitroarginine-based dipeptide inhibitors are highly selective for neuronal nitric oxide synthase (nNOS) over the endothelial isoform (eNOS). Crystal structures of these dipeptides bound to both isoforms revealed two different conformations, curled in nNOS and extended in eNOS, corresponding to higher and lower binding affinity to the two isoforms, respectively. In previous studies we found that the primary reason for selectivity is that Asp597 in nNOS, which is Asn368 in eNOS, provides greater electrostatic stabilization in the inhibitor complex. While this is the case for smaller dipeptide inhibitors, electrostatic stabilization may no longer be the sole determinant for isoform selectivity with bulkier dipeptide inhibitors. Another residue farther away from the active site, Met336 in nNOS (Val106 in eNOS), is in contact with bulkier dipeptide inhibitors. Double mutants were made to exchange the D597/M336 pair in nNOS with N368/V106 in eNOS. Here we report crystal structures and inhibition constants for bulkier dipeptide inhibitors bound to nNOS and eNOS that illustrate the important role played by residues near the entry to the active site in isoform selective inhibition.