Chromophore Structure of Cyanobacterial Phytochrome Cph1 in the Pr State: Reconciling Structural and Spectroscopic Data by QM/MM Calculations

A quantum mechanics (QM)/molecular mechanics (MM) hybrid method was applied to the Pr state of the cyanobacterial phytochrome Cph1 to calculate the Raman spectra of the bound PCB cofactor. Two QM/MM models were derived from the atomic coordinates of the crystal structure. The models differed in the protonation site of His²⁶⁰ in the chromophore-binding pocket such that either the δ-nitrogen (M-HSD) or the ɛ-nitrogen (M-HSE) carried a hydrogen. The optimized structures of the two models display small differences specifically in the orientation of His²⁶⁰ with respect to the PCB cofactor and the hydrogen bond network at the cofactor-binding site. For both models, the calculated Raman spectra of the cofactor reveal a good overall agreement with the experimental resonance Raman (RR) spectra obtained from Cph1 in the crystalline state and in solution, including Cph1 adducts with isotopically labeled PCB. However, a distinctly better reproduction of important details in the experimental spectra is provided by the M-HSD model, which therefore may represent an improved structure of the cofactor site. Thus, QM/MM calculations of chromoproteins may allow for refining crystal structure models in the chromophore-binding pocket guided by the comparison with experimental RR spectra. Analysis of the calculated and experimental spectra also allowed us to identify and assign the modes that sensitively respond to chromophore-protein interactions. The most pronounced effect was noted for the stretching mode of the methine bridge A-B adjacent to the covalent attachment site of PCB. Due a distinct narrowing of the A-B methine bridge bond angle, this mode undergoes a large frequency upshift as compared with the spectrum obtained by QM calculations for the chromophore in vacuo. This protein-induced distortion of the PCB geometry is the main origin of a previous erroneous interpretation of the RR spectra based on QM calculations of the isolated cofactor.Abbreviations: Agp1, phytochrome from Agrobacterium tumefaciens; α-CPC, α-subunit of C-phycocyanin; BV, biliverdin IXα; B3LYP, three-parameter exchange functional according to Becke, Lee, Yang, and Parr; DFT, density functional theory; DrBphP, phytochrome from Deinococcus radiodurans; GAF, domain found in cGMP-specific phosphodiesterases; MM, molecular mechanics; MD, molecular dynamics; N-H ip, N-H in-plane bending; PCB, phycocyanobilin; PED, potential energy distribution; phyA, plant phytochrome; Pr, Pfr, red- and far-red absorbing parent states of phytochrome; PΦB, phytochromobilin; QM, quantum mechanics; RMSD, root mean-square deviation; RR, resonance Raman     

Theozymes and compuzymes: theoretical models for biological catalysis

A theozyme is a theoretical enzyme constructed by computing the optimal geometry for transition-state stabilization by functional groups. It is created in order to permit quantitative assessment of catalytic function. Theozymes have been used to elucidate the role of transition-state stabilization in the mechanisms underlying enzyme- and antibody-catalyzed hydroxyepoxide cyclizations, eliminations and decarboxylations, peptide and ester hydrolyses, and pericyclic and radical reactions. The enzymes studied include orotodine monophosphate decarboxylase, HIV protease and ribonucleotide reductase.     

Atlantic salmon (Salmo salar) of the Pigou and Bouleau Rivers,Quebec

Synopsis Juvenile Atlantic salmon of the Pigou and Bouleau Rivers, Quebec, were studied during the summer of 1972 and 1973. Growth increments for Pigou salmon averaged 36–50 mm yr^–1 and smolts averaged 2.9 yrs old. Bouleau salmon grew slower (26–41 mm yr^–1) and became smolts at a slightly older mean age (3.1 yrs). Mature male parr were more abundant in all age-groups from the Plgou River, possibly because of the faster growth. In terms of management, the Pigou River has little potential for increased salmon production because of limited habitat. On the other hand, the Bouleau River has considerable potential, and salmon production could be increased if the upper reaches were made accessible to migrating salmon.Contribution number 36 of the Matamek Research Station, Woods Hole Oceanographic Institute.     

Mating success of alternative maturation phenotypes in male Atlantic salmon,Salmo salar

Summary Mature male parr successfully fertilized eggs of anadromous female Atlantic salmon, Salmo salar, in competition with anadromous males under simulated natural conditions. Mating situations were created in which mature male parr and anadromous males competing for the opportunity to spawn with an anadromous female differed in allelic forms of the same enzyme. Females deposited eggs into a sequence of 3 or 4 eggs nests. The mean proportion of eggs in a redd fertilized by parr increased with increasing numbers of parr present at a redd, reaching 23% at male parr: anadromous male ratios of 20:1. Single male parr fertilized, on average, 5% of the eggs in a redd. The proportion of eggs in an egg nest fertilized by parr also depended upon the order of egg nest construction, such that parr mating success was highest at the initial nest constructed and lowest at the final nest. Parr have relatively high fertilization success for their size when compared with the smaller maturation phenotype of other salmonids.     

Individual growth and phase differentiation of lacustrine masu salmon, Oncorhynchus masou, under artificial rearing conditions

 In lacustrine masu salmon, Oncorhynchus masou, originated from anadromous fish and inhabiting an artificial lake (Shumarinai Lake), we examined the relationship between individual growth during the juvenile stage and phase differentiation under artificial rearing conditions. In females, the mean fork length of potential (subsequent) 1+ smolts and potential 1+ parr (1+ parr show fish that neither smolted nor matured until 1+ autumn) always differed after their first summer (0+ summer), the former being larger. In males, the juveniles that grew faster during their first spring became 0+ mature male parr. After their first summer, potential 1+ smolts were always larger in body length than potential 1+ mature parr and potential 1+ parr. These results were similar to previous reports of anadromous masu salmon, suggesting that the lacustrine masu salmon studied seems to have maintained the phase differentiation as in the original fish, likely because only 60 years have passed since the formation of the lacustrine population.     

EROD activity in gill filaments of anadromous and marine fish as a biomarker of dioxin-like pollutants

The applicability of a gill filament-based ethoxyresorufin O-deethylase (EROD) assay, originally developed in rainbow trout, was examined in Atlantic salmon (Salmo salar), Arctic charr (Salvelinus alpinus), Atlantic cod (Gadus morhua), saithe (Pollachius virens) and spotted wolffish (Anarhichas minor). All species but spotted wolffish showed strong EROD induction in tip pieces of gill filaments following 48 h of exposure to waterborne beta-naphthoflavone. Atlantic salmon parr, smolts held in freshwater and smolts transferred to seawater showed EROD induction of similar magnitude. Arctic charr, differing 11-fold in body weight, showed similar EROD activities as expressed per gill filament tip. Laboratory exposure of saithe to water and sediments collected at polluted sites, resulted in strong EROD induction. In conclusion, the gill filament assay seems useful for monitoring exposure to aryl hydrocarbon receptor agonists in various species. Furthermore, smoltification status, water salinity and body size proved to have minor influence on gill filament EROD activity. However, the results in spotted wolffish show that some species may be less suitable for monitoring using the gill assay. Assessment of gill filament EROD activity in fish exposed to polluted water and sediments in the laboratory proved to be an easy and cost-effective way to survey pollution with dioxin-like chemicals.     

Inclusion of water temperature in a fuzzy logic Atlantic salmon (Salmo salar) parr habitat model

As water temperature is projected to increase in the next decades and its rise is clearly identified as a threat for cold water fish species, it is necessary to adapt and optimize the tools allowing to assess the quantity and quality of habitats with the inclusion of temperature. In this paper, a fuzzy logic habitat model was improved by adding water temperature as a key determinant of juvenile Atlantic salmon parr habitat quality. First, salmon experts were consulted to gather their knowledge of salmon parr habitat, then the model was validated with juvenile salmon electrofishing data collected on the Sainte-Marguerite, Matapedia and Petite-Cascapedia rivers (Québec, Canada). The model indicates that when thermal contrasts exist at a site, cooler temperature offered better quality of habitat. Our field data show that when offered the choice, salmon parr significantly preferred to avoid both cold areas (<15 °C) and warm areas (>20.5 °C). Because such thermal contrasts were not consistently present among the sites sampled, the model was only validated for less than 60% of the sites. The results nevertheless indicate a significant correlation between median Habitat Quality Index and parr density for the Sainte-Marguerite River (R² = 0.38). A less important, albeit significant (F-test; p = 0.036) relationship was observed for the Petite-Cascapedia river (R² = 0.14). In all instances, the four-variable (depth, velocity, substrate size and temperature) model provided a better explanation of parr density than a similar model excluding water temperature.     

A quantum mechanics/molecular mechanics study of the tyrosine residue, TyrD, of Photosystem II

QM/MM calculations have been used to monitor the oxidation of the D2-Tyr160, Tyr_D, residue involved in redox reactions in Photosystem II. The results indicate that in the reduced form the residue is involved in hydrogen bond donation via its phenolic head group to the τ-nitrogen of the neighboring D2-His189 residue. Oxidation to form the radical is accompanied by spontaneous transfer of the phenolic hydrogen to the τ-nitrogen of D2-His189 leading to the formation of a tyrosyl-imidazolium ion complex. Deprotonation of the imidazolium ion leads to the formation of a tyrosyl-imidazole neutral hydrogen-bonded complex. Comparison of calculated and experimental hyperfine coupling tensors and g-tensors suggests that the neutral imidazole complex is formed at physiological temperatures while the imidazolium complex may be stabilized at cryogenic temperatures.     

Influence of natural and regulated streamflow on survival of brown trout (Salmo trutta L.) in a chalkstream

Synopsis Numbers of age 0± trout in October, and annual survival of fish over 2 years old, were closely correlated with mean April flow (discharge) in a groundwater-fed stream. A pilot flow regulation scheme, which enhanced flows from May to September in a drought year, failed to increase survival.Hampshire Rivers Division, Southern Water Authority