Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10).
A triple mutant of sperm whale myoglobin (Mb) [Leu(B10) --> Tyr, His(E7) --> Gln, and Thr(E10) --> Arg, called Mb-YQR], investigated by stopped-flow, laser photolysis, crystallography, and molecular dynamics (MD) simulations, proved to be quite unusual. Rebinding of photodissociated NO, O2, and CO from within the protein (in a "geminate" mode) allows us to reach general conclusions about dynamics and cavities in proteins. The 3D structure of oxy Mb-YQR shows that bound O2 makes two H-bonds with Tyr(B10)29 and Gln(E7)64; on deoxygenation, these two residues move toward the space occupied by O2. The bimolecular rate constant for NO binding is the same as for wild-type, but those for CO and O2 binding are reduced 10-fold. While there is no geminate recombination with O2 and CO, geminate rebinding of NO displays an unusually large and very slow component, which is pretty much abolished in the presence of xenon. These results and MD simulations suggest that the ligand migrates in the protein matrix to a major "secondary site," located beneath Tyr(B10)29 and accessible via the motion of Ile(G8)107; this site is different from the "primary site" identified by others who investigated the photolyzed state of wild-type Mb by crystallography. Our hypothesis may rationalize the O2 binding properties of Mb-YQR, and more generally to propose a mechanism of control of ligand binding and dissociation in hemeproteins based on the dynamics of side chains that may (or may not) allow access to and direct temporary sequestration of the dissociated ligand in a docking site within the protein. This interpretation suggests that very fast (picosecond) fluctuations of amino acid side chains may play a crucial role in controlling O2 delivery to tissue at a rate compatible with physiology. (+info
Declining survival probability threatens the North Atlantic right whale.
The North Atlantic northern right whale (Eubalaena glacialis) is considered the most endangered large whale species. Its population has recovered only slowly since the cessation of commercial whaling and numbers about 300 individuals. We applied mark-recapture statistics to a catalog of photographically identified individuals to obtain the first statistically rigorous estimates of survival probability for this population. Crude survival decreased from about 0.99 per year in 1980 to about 0.94 in 1994. We combined this survival trend with a reported decrease in reproductive rate into a branching process model to compute population growth rate and extinction probability. Population growth rate declined from about 1. 053 in 1980 to about 0.976 in 1994. Under current conditions the population is doomed to extinction; an upper bound on the expected time to extinction is 191 years. The most effective way to improve the prospects of the population is to reduce mortality. The right whale is at risk from entanglement in fishing gear and from collisions with ships. Reducing this human-caused mortality is essential to the viability of this population. (+info
Sex-biased dispersal in sperm whales: contrasting mitochondrial and nuclear genetic structure of global populations.
The social organization of most mammals is characterized by female philopatry and male dispersal. Such sex-biased dispersal can cause the genetic structure of populations to differ between the maternally inherited mitochondrial DNA (mtDNA) and the bi-parental nuclear genome. Here we report on the global genetic structure of oceanic populations of the sperm whale, one of the most widely distributed mammalian species. Groups of females and juveniles are mainly found at low latitudes, while males reach polar waters, returning to tropical and subtropical waters to breed. In comparisons between oceans, we did not find significant heterogeneity in allele frequencies of microsatellite loci (exact test; p = 0.23). Estimates of GST = 0.001 and RST = 0.005 also indicated negligible if any nuclear DNA differentiation. We have previously reported significant differentiation between oceans in mtDNA sequences. These contrasting patterns suggest that interoceanic movements have been more prevalent among males than among females, consistent with observations of females being the philopatric sex and having a more limited latitudinal distribution than males. Consequently, the typical mammalian dispersal pattern may have operated on a global scale in sperm whales. (+info
Quench-flow experiments combined with mass spectrometry show apomyoglobin folds through and obligatory intermediate.
Folding of apomyoglobin is characterized by formation of a compact intermediate that contains substantial helicity. To determine whether this intermediate is obligatory or whether the protein can fold directly into the native state via an alternate parallel pathway, we have combined quench-flow hydrogen-exchange pulse labeling techniques with electrospray ionization mass spectrometry. The mass spectra of apomyoglobin obtained at various refolding times suggest that apomyoglobin indeed folds through a single pathway containing an obligatory intermediate with a significant hydrogen-bonded secondary structure content. (+info
Purification and properties of whale thyroid-stimulating hormone III. Properties of isolated multiple components.
Properties of the four purified components of whale thyroid-stimulating hormone (TSH) have been compared. The amino acid composition shows close similarity among these components. Their hexosamine and sialic acid contents are of the same magnitude, whereas the neutral sugar composition differs somewhat from each other. The molecular weight of whale TSH determined by sedimentation equilibrium is 29,000, and no difference in molecular weight as well as in Stokes radius as determined by gel filtration has been detected among these four components. The amino acid and carbohydrate compositions of whale TSH resemble those of TSH from other species, especially those of non-primate mammalian TSH. Whale TSH contains, unlike bovine TSH but like human TSH, 1-2 residues of sialic acid as a constituent carbohydrate. (+info
Abiotrophia balaenopterae sp. nov., isolated from the minke whale (Balaenoptera acutorostrata).
Phenotypic and phylogenetic studies were performed on a hitherto undescribed micro-organism isolated from a minke whale (Balaenoptera acutorostrata). Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strain constituted a new subline close to, but distinct from, Abiotrophia adiacens and Abiotrophia elegans. The unknown bacterium was readily distinguished from these two Abiotrophia species by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Abiotrophia balaenopterae sp. nov., the type strain of which is M1975/96/1T (= CCUG 37380T). (+info
Immunohistological distributions of fibronectin, tenascin, type I, III and IV collagens, and laminin during tooth development and degeneration in fetuses of minke whale, Balaenoptera acutorostrata.
The immunohistological distributions of fibronectin, tenascin, type I, III and IV collagens, and laminin were observed in the tooth buds of fetuses of minke whale, Balaenoptera acutorostrata. Distributions of extracellular matrices (ECMs) examined in this study except for tenascin were generally similar to those of terrestrial mammalian species during development of the tooth bud. Tenascin in the fetuses of minke whale showed characteristic distributions in the dental lamina and the enamel organ in the early tooth developmental stage. In the physiological degeneration stage of tooth bud development, immunoreactivity of the ECMs were very weakly and limitedly detected in the dental papilla and the surrounding mesenchyme. Immunoreactivity of tenascin and type I and III collagens were positively detected in the developing baleen plate germ which was associated with the degenerating tooth bud. These findings suggested that expressions of the ECMs were related to the formation of the tooth bud and baleen plate germ, and that the lack of the ECMs was related to the degeneration of the tooth bud in the fetal minke whale. (+info
A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin.
The vibrational energy relaxation of dissociated carbon monoxide in the heme pocket of sperm whale myoglobin has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the delta- and epsilon-tautomers of the distal histidine, His64. Vibrational population relaxation times were estimated using the Landau-Teller model. For carbon monoxide (CO) in the myoglobin epsilon-tautomer, for a frequency of omega0 = 2131 cm-1 corresponding to the B1 state, T1epsilon(B1) = 640 +/- 185 ps, and for a frequency of omega0 = 2119 cm-1 corresponding to the B2 state, T1epsilon(B2) = 590 +/- 175 ps. Although the CO relaxation rates in both the epsilon- and delta-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the delta-tautomer. For CO in the myoglobin delta-tautomer, it was found that the relaxation times were identical within error for the two CO substate frequencies, T1delta(B1) = 335 +/- 115 ps and T1delta(B2) = 330 +/- 145 ps. These simulation results are in reasonable agreement with experimental results of Anfinrud and coworkers (unpublished results). Normal mode calculations were used to identify the dominant coupling between the protein and CO molecules. The calculations suggest that the residues of the myoglobin pocket, acting as a first solvation shell to the CO molecule, contribute the primary "doorway" modes in the vibrational relaxation of the oscillator. (+info