Hydrogen bonding in globular proteins.

A global census of the hydrogen bonds in 42 X-ray-elucidated proteins was taken and the following demographic trends identified: (1) Most hydrogen bonds are local, i.e. between partners that are close in sequence, the primary exception being hydrogen-bonded ion pairs. (2) Most hydrogen bonds are between backbone atoms in the protein, an average of 68%. (3) All proteins studied have extensive hydrogen-bonded secondary structure, an average of 82%. (4) Almost all backbone hydrogen bonds are within single elements of secondary structure. An approximate rule of thirds applies: slightly more than one-third (37%) form i----i--3 hydrogen bonds, almost one-third (32%) form i----i--4 hydrogen bonds, and slightly less than one-third (26%) reside in paired strands of beta-sheet. The remaining 5% are not wholly within an individual helix, turn or sheet. (5) Side-chain to backbone hydrogen bonds are clustered at helix-capping positions. (6) An extensive network of hydrogen bonds is present in helices. (7) To a close approximation, the total number of hydrogen bonds is a simple function of a protein's helix and sheet content. (8) A unique quantity, termed the reduced number of hydrogen bonds, is defined as the maximum number of hydrogen bonds possible when every donor:acceptor pair is constrained to be 1:1. This quantity scales linearly with chain length, with 0.71 reduced hydrogen bond per residue. Implications of these results for pathways of protein folding are discussed.     

Respiratory and osmoregulatory responses of the hermit crab, Clibanarius vittatus (Bosc), to salinity changes

Intertidal hermit crabs were stepwise acclimated to 10, 20, and 30‰ salinity (S) and 21 ± 1 °C. Hemolymph osmolality, sodium, chloride, and magnesium were isosmotic (isoionic) to ambient sea water at 30‰ and hyperosmotic (hyperionic) at 20 and 10‰ S, while hemolymph potassium was significantly hyperionic in all acclimation salinities. Total body water did not differ significantly at any acclimation salinity. Oxygen uptake rates were higher in summer-than winter-adapted crabs. No salinity effect on oxygen consumption occurred in winter-adapted individuals. Summer-adapted, 30‰ acclimated crabs had a significantly lower oxygen consumption rate than those acclimated 10 and 20‰ S. Crabs exposed to 30 10 30‰ and 10 30 10‰ semidiurnal (12 h) and diurnal (24.8 h) fluctuating salinity regimes showed variable osmoregulatory and respiratory responses. Hemolymph osmolality followed the osmolality of the fluctuating ambient sea water in all cases, but was regulated hyperosmotically. Hemolymph sodium, chloride, and magnesium concentrations were similar to hemolymph osmolality changes. Sodium levels fluctuated the least. Hemolymph potassium was regulated hyperionically during all fluctuation patters, but corresponded to sea water potassium only under diurnal conditions. The osmoregulatory ability of Clibanarius vittatus (Bosc) resembles that reported for several euryhaline brachyuran species. The time course of normalized oxygen consumption rate changed inversely with salinity under semidiurnal and diurnal 10 30 10‰ S fluctuations. Patterns of 30 10 30‰ S cycles had no effect on oxygen consumption rate time course changes. The average hourly oxygen consumption rates during both semidiurnal fluctuations were significantly lower than respective control rates, but no statistical difference was observed under diurnal conditions.     

A covalently bound photoisomerizable agonist. Comparison with reversibly bound agonists at electrophorus electroplaques

After disulphide bonds are reduced with dithiothreitol, trans-3- (α-bromomethyl)-3’-[α- (trimethylammonium)methyl]azobenzene (trans-QBr) alkylates a sulfhydryl group on receptors. The membrane conductance induced by this “tethered agonist” shares many properties with that induced by reversible agonists. Equilibrium conductance increases as the membrane potential is made more negative; the voltage sensitivity resembles that seen with 50 [mu]M carbachol. Voltage- jump relaxations follow an exponential time-course; the rate constants are about twice as large as those seen with 50 μM carbachol and have the same voltage and temperature sensitivity. With reversible agonists, the rate of channel opening increases with the frequency of agonist-receptor collisions: with tethered trans-Qbr, this rate depends only on intramolecular events. In comparison to the conductance induced by reversible agonists, the QBr-induced conductance is at least 10-fold less sensitive to competitive blockade by tubocurarine and roughly as sensitive to “open-channel blockade” bu QX-222. Light-flash experiments with tethered QBr resemble those with the reversible photoisomerizable agonist, 3,3’,bis-[α-(trimethylammonium)methyl]azobenzene (Bis-Q): the conductance is increased by cis {arrow} trans photoisomerizations and decreased by trans {arrow} cis photoisomerizations. As with Bis-Q, ligh-flash relaxations have the same rate constant as voltage-jump relaxations. Receptors with tethered trans isomer. By comparing the agonist-induced conductance with the cis/tans ratio, we conclude that each channel’s activation is determined by the configuration of a single tethered QBr molecule. The QBr-induced conductance shows slow decreases (time constant, several hundred milliseconds), which can be partially reversed by flashes. The similarities suggest that the same rate-limiting step governs the opening and closing of channels for both reversible and tethered agonists. Therefore, this step is probably not the initial encounter between agonist and receptor molecules.     

Parasitism of Leptasterias spp. (Echinodermata: Asteroidea) by the ciliated protozoan Orchitophrya stellarum (Scuticociliata)

Abstract. The parasitic ciliate Orchitophrya stellarum was found in the testes of brooding, winter-spawning Leptasterias spp. from San Juan Island, Washington, but not in the testes of Leptasterias spp. from the Lynn Canal, Alaska. Dense populations of the ciliate were localized within the fuller areas of testes, where sperm counts were significantly reduced. The ciliates were loaded with phagosomes, some of which contained sperms in various stages of digestion. Leptasterias spp. are not as severely impacted by this ciliated protozoan parasite as Pisaster ochraceus. Leptasterias spp. may serve as seasonal hosts for O. stellarum ; this ciliate lives in seawater and in ripe males of winter-brooding and spring-summer broadcasting sea stars. The wet weight of parasitized and non-parasitized males did not differ. The sex ratio did not deviate from the expected (1:1) in any population except at Point Louisa, Alaska, where males outnumbered females. Testis indexes of parasitized males from 2 of the 4 locations on San Juan Island, Washington were significantly reduced relative to non-parasitized males, indicating a loss of sperm output during spawning.     

Mechanism of Na‐Ion Storage in Hard Carbon Anodes Revealed by Heteroatom Doping

Hard carbon is the leading candidate anode for commercialization of Na‐ion batteries. Hard carbon has a unique local atomic structure, which is composed of nanodomains of layered rumpled sheets that have short‐range local order resembling graphene within each layer, but complete disorder along the c‐axis between layers. A primary challenge holding back the development of Na‐ion batteries is that a complete understanding of the structure–capacity correlations of Na‐ion storage in hard carbon has remained elusive. This article presents two key discoveries: first, the characteristics of hard carbons structure can be modified systematically by heteroatom doping, and second, that these structural changes greatly affect Na‐ion storage properties, which reveals the mechanisms for Na storage in hard carbon. Specifically, via P or S doping, the interlayer spacing is dilated, which extends the low‐voltage plateau capacity, while increasing the defect concentrations with P or B doping leads to higher sloping sodiation capacity. The combined experimental studies and first principles calculations reveal that it is the Na‐ion‐defect binding that corresponds to the sloping capacity, while the Na intercalation between graphenic layers causes the low‐potential plateau capacity. The understanding suggests a new design principle of hard carbon anode: more reversibly binding defects and dilated turbostratic domains, given that the specific surface area is maintained low.     

Cytosolic calcium, calcium fluxes, and regulation of alveolar macrophage superoxide anion production

The recently available compound quin-2, which acts as a high affinity fluorescent indicator for calcium in the cytosol, was used to examine the role of calcium mobilization in the alveolar macrophage during the stimulation of 0-2 production by the tripeptide N-formyl norleucyl leucyl phenylalanine (FNLLP). After preloading with quin-2, the production of 0-2 was measured in conjunction with the transfer of 45Ca+2 and changes in quin-2 fluorescence upon stimulation with FNLLP. When cells were maintained in low (10 microM) extracellular calcium medium the presence of 1.5 mM quin-2 in the cytosolic space partially inhibited the rate of 0-2 production upon stimulation by FNLLP. Addition of 1 mM Ca+2 to the medium prior to stimulation rapidly restored the cell's capability to produce 0-2 upon stimulation at rates equal to control and extended the duration of stimulated 0-2 production as well. Quin-2 fluorescence measurements indicated an increase in cytosolic Ca+2 upon stimulation with FNLLP. This increase was lowest under conditions in which 0-2 production was inhibited. The addition of 1 mM Ca+2 to the medium caused by itself a rapid but transient increase in cytosolic Ca+2 as measured with quin-2 without stimulating 0-2 production. This intracellularly redistributed calcium was determined to be the source of the greater increase in cytosolic calcium during stimulation in the presence of high extracellular calcium. Measurements of 45Ca+2 transfer demonstrated a buffering of cytosolic Ca+2 changes by quin-2, which in low calcium medium could deplete calcium stores. It is suggested that this effect, prior to stimulation, was responsible for the mitigated 0-2 response for those cells maintained in low calcium medium, wherein calcium stores could not be replenished. These results suggested that the cell's mechanism for regulating cytosolic and bound calcium concentrations may also play an integral role in its normal mechanism for stimulated 0-2 production. They further support the postulate that the commonly observed rise in the concentration of calcium in the cytosol upon formyl peptide stimulation is a concomitant but nonregulatory event only.     

Genome-wide differentially methylated genes in prostate cancer tissues from African-American and Caucasian men

Increasing evidence suggests that aberrant DNA methylation changes may contribute to prostate cancer (PCa) ethnic disparity. To comprehensively identify DNA methylation alterations in PCa disparity, we used the Illumina 450K methylation platform to interrogate the methylation status of 485,577 CpG sites focusing on gene-associated regions of the human genome. Genomic DNA from African-American (AA; 7 normal and 3 cancers) and Caucasian (Cau; 8 normal and 3 cancers) was used in the analysis. Hierarchical clustering analysis identified probe-sets unique to AA and Cau samples, as well as common to both. We selected 25 promoter-associated novel CpG sites most differentially methylated by race (fold change > 1.5-fold; adjusted P < 0.05) and compared the β-value of these sites provided by the Illumina, Inc. array with quantitative methylation obtained by pyrosequencing in 7 prostate cell lines. We found very good concordance of the methylation levels between β-value and pyrosequencing. Gene expression analysis using qRT-PCR in a subset of 8 genes after treatment with 5-aza-2′-deoxycytidine and/or trichostatin showed up-regulation of gene expression in PCa cells. Quantitative analysis of 4 genes, SNRPN, SHANK2, MST1R, and ABCG5, in matched normal and PCa tissues derived from AA and Cau PCa patients demonstrated differential promoter methylation and concomitant differences in mRNA expression in prostate tissues from AA vs. Cau. Regression analysis in normal and PCa tissues as a function of race showed significantly higher methylation prevalence for SNRPN (P = 0.012), MST1R (P = 0.038), and ABCG5 (P < 0.0002) for AA vs. Cau samples. We selected the ABCG5 and SNRPN genes and verified their biological functions by Western blot analysis and siRNA gene knockout effects on cell proliferation and invasion in 4 PCa cell lines (2 AA and 2 Cau patients-derived lines). Knockdown of either ABCG5 or SNRPN resulted in a significant decrease in both invasion and proliferation in Cau PCa cell lines but we did not observe these remarkable loss-of-function effects in AA PCa cell lines. Our study demonstrates how differential genome-wide DNA methylation levels influence gene expression and biological functions in AA and Cau PCa.     

The SH2B1 adaptor protein associates with a proximal region of the erythropoietin receptor

Gene targeting experiments have shown that the cytokine erythropoietin (EPO), its cognate erythropoietin receptor (EPO-R), and associated Janus tyrosine kinase, JAK2, are all essential for erythropoiesis. Structural-functional and murine knock-in experiments have suggested that EPO-R Tyr-343 is important in EPO-mediated mitogenesis. Although Stat5 binds to EPO-R phosphotyrosine 343, the initial Stat5-deficient mice did not have profound erythroid abnormalities suggesting that additional Src homology 2 (SH2) domain-containing effectors may bind to EPO-R Tyr-343 and couple to downstream signaling pathways. We have utilized cloning of ligand target (COLT) screening to demonstrate that EPO-R Tyr(P)-343 and Tyr(P)-401 bind to the SH2 domain-containing adaptor protein SH2B1β. Immunoprecipitation and in vitro mixing experiments reveal that EPO-R binds to SH2B1 in an SH2 domain-dependent manner and that the sequence that confers SH2B1 binding to the EPO-R is pYXXL. Previous studies have shown that SH2B1 binds directly to JAK2, but we show that in hematopoietic cells, SH2B1β preferentially associates with the EPO-R. SH2B1 is capable of constitutive association with EPO-R, which is necessary for its optimal SH2-dependent recruitment to EPO-R-Tyr(P)-343/Tyr(P)-401. We also demonstrate that SH2B1 is responsive to EPO stimulation and becomes phosphorylated, most likely on serines/threonines, in an EPO dose- and time-dependent manner. In the absence of SH2B1, we observe enhanced activation of signaling pathways downstream of the EPO-R, indicating that SH2B1 is a negative regulator of EPO signaling.     

Role of hydration in the binding of lac repressor to DNA

The osmotic stress technique was used to measure changes in macromolecular hydration that accompany binding of wild-type Escherichia coli lactose (lac) repressor to its regulatory site (operator O1) in the lac promoter and its transfer from site O1 to nonspecific DNA. Binding at O1 is accompanied by the net release of 260 +/- 32 water molecules. If all are released from macromolecular surfaces, this result is consistent with a net reduction of solvent-accessible surface area of 2370 +/- 550 A. This area is only slightly smaller than the macromolecular interface calculated for a crystalline repressor dimer-O1 complex but is significantly smaller than that for the corresponding complex with the symmetrical optimized O(sym) operator. The transfer of repressor from site O1 to nonspecific DNA is accompanied by the net uptake of 93 +/- 10 water molecules. Together these results imply that formation of a nonspecific complex is accompanied by the net release of 165 +/- 43 water molecules. The enhanced stabilities of repressor-DNA complexes with increasing osmolality may contribute to the ability of Escherichia coli cells to tolerate dehydration and/or high external salt concentrations.     

Effects of salinity on the respiration and heart rate of the common mussel, Mytilus edulis L., and the black chiton, Katherina tunicata (Wood)

The rate of oxygen consumption of stepwise acclimated Mytilus edulis L. increased linearly from 30 to 10‰ salinity (S) while that of Katherina tunicata (Wood) was not significantly different between 10 and 30‰ S. Heart rate was 21–22 and 17–18 beats m^?1 in Mytilus edulis and Katherina tunicata, respectively, and no difference was found in the heart rate of either species acclimated stepwise to 10, 20 or 30‰ S. The average oxygen consumption rate of Mytilus edulis exposed to 12 h, 30-10-30 and 10-30-10‰ S cycles of fluctuating salinity was significantly lower than the respective control rate: there was a similar response during the 30-10-30‰ S cycle in Katherina tunicata. The respiration rate of Mytilus edulis and Katherina tunicata declined as salinity deviated from the control salinity and increased as salinity returned to the control salinity. The rate of oxygen consumption by K. tunicata varied directly with the ambient salinity during the 10-30-10‰ S cycle. The average heart rate of Mytilus edulis was significantly lower during cyclic changes in salinity than at the respective control salinities; a similar relationship existed for Katherina tunicata during the 10-30-10‰ S cycle. Heart rate of Mytilus edulis varied in a parallel manner with oxygen consumption during both cycles. Katherina tunicata heart rate was relatively constant and could not be fitted to a regression line during the 10-30-10‰ S cycle. The normalized heart rate increased to 113% of control at 10‰ S of the 30-10-30‰ S cycle and returned to the control rate by 12 h. The oxygen consumption and heart rate of these two species are not directly coupled to regulation of water volume because different responses are observed with respect to salinity although there is poor water volume regulation in both species.