Re-evaluation of the 18 non-human protein standards used to create the empirical statistical model for decoy library searching.

The Empirical Statistical Model (ESM) for decoy library searching fused the expected amino acid sequence of 18 non-human protein standards to a human decoy library. The ESM assumed a priori the standards were pure such that only the 18 nominal proteins were true positive, all other proteins were false positive, there was no overlap in the peptides of non-human proteins versus human proteins, and that the score distribution of individual peptides would resolve true positive from false positive results or noise. The results of random and independent sampling by LC-ESI-MS/MS indicated that the fundamental assumptions of the ESM were not in good agreement with the actual purity of the commercial test standards and so the method showed a 99.7% false negative rate. The ESM for decoy library searching apparently showed poor agreement with SDS-PAGE using silver staining, goodness of fit of MS/MS spectra by X!TANDEM, FDR correction by Benjamini and Hochberg, or comparison to the observation frequency of null random MS/MS spectra, that all confirmed the standards contain hundreds of proteins with a low FDR of primary structural identification. The protein observation frequency increased with abundance and the log10 precursor intensity distributions were Gaussian and nearly ideal for relative quantification.

Re-evaluation of the rabbit myosin protein standard used to create the empirical statistical model for decoy library searching.

A Rabbit myosin standard, like that used to create the empirical statistical model, was randomly and independently sampled by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) with a linear quadrupole ion trap. The rabbit myosin protein standard appeared pure by SDS-PAGE and CBBR staining but showed many other proteins by silver staining. The LC-MS intensity from myosin and IgG samples were above the 99% safe limit of detection and quantification computed from 36 blank LC-ESI-MS/MS runs. The myosin contained ≤406 Gene Symbols, open reading frames or loci where 79 protein types showed ≥3 peptides from X!TANDEM. Myosins, actin, troponin, other proteins showed 95%-100% homology between the rabbit versus the human decoy library. The myosin protein complex from STRING was true positive compared to random or noise spectra MS/MS with a low type I error (p-value) and low FDR (q-value) computed in R. SDS-PAGE, Western blot, comparison to random and noise MS/MS spectra, X!TANDEM p-values, FDR corrected q-values, and STRING all agreed that the error rate of LC-ESI-MS/MS with a quadrupole ion trap is far below that assumed a priori by the design of the empirical statistical model for decoy library searching.

Enhanced activity of inositol-1,4,5-trisphosphate receptors in atrial myocytes of atrial fibrillation patients.

The roles of inositol-1,4,5-trisphosphate receptors (IP3Rs) in arrhythmia are not fully understood, especially in human beings. Recently, the reported upregulated expression of IP3Rs in atrial myocytes of atrial fibrillation (AF) subjects suggested that IP3Rs might be associated with AF. To directly understand the roles of IP3Rs in AF, we have investigated the IP3R-dependent Ca2+ events as well as the cross-talk between IP3Rs and ryanodine receptors (RyRs) in permeabilized atrial myocytes of AF and normal sinus rhythm (NSR) patients by Ca2+ imaging. In the presence of tetracaine, IP(3)R-dependent Ca2+ events in AF atrial myocytes showed increased frequency, delayed termination and broadened width, compared with NSR myocytes. Moreover, when RyRs were not inhibited, IP3 or adenophostin induced an outburst of RyR-dependent spontaneous Ca2+ sparks with the altered spatial-temporal characteristics. The activation of IP3Rs also enhanced Ca2+ waves. These effects on RyR-dependent Ca2+ signaling were significantly stronger in AF myocytes than in NSR cells and were completely blocked by 2-aminoethoxydiphenyl borate. Thus, our results suggested not only an enhanced activity of IP3Rs but also an elevated cross-talk between IP3R- and RyR-mediated Ca2+ signaling in atrial myocytes of human AF patients, a reflection of altered function of IP3Rs in AF.

Ryanodine receptor-mediated Ca2+ events in atrial myocytes of patients with atrial fibrillation.

BACKGROUND: Many alterations in sarcoplasmic reticulum Ca(2+) handling proteins in atrial myocytes have been associated with atrial fibrillation (AF) in clinical patients, whereas the functional consequences of these alterations mostly remain unclear. METHODS AND RESULTS: To know whether or not ryanodine receptor (RyR)-mediated intracellular Ca(2+) events in AF atrial myocytes are affected by protein alterations, we investigated spontaneous Ca(2+) sparks and Ca(2+) waves in intact and permeabilized atrial myocytes of AF patients (n(patients) = 21) and normal sinus rhythm (NSR) patients (n(patients) = 22) by laser scanning confocal microscopy. It was found that the frequency, amplitude and rise time of Ca(2+) sparks were comparable between AF and NSR groups, while full width and full duration at half maximum intensity significantly increased in the AF group. Along with these changes, the frequency of small and global Ca(2+) waves increased in AF atrial myocytes. CONCLUSIONS: Our results clearly indicated that the spatiotemporal properties but not the frequency of Ca(2+) sparks were affected in AF atrial myocytes. In addition, the frequency of Ca(2+) waves increased. This profile of the alterations in RyR-mediated Ca(2+) events in AF atrial myocytes was different from previous studies. The underlying mechanisms, as well as possible reasons for this discrepancy, were discussed.

Oligomeric interaction between ryanodine receptors: potential role in Ca(2+) release.

Receptor proteins in both eukaryotic and prokaryotic cells often form regular lattice or array in the membrane. Recent theoretical analyses indicate that such arrays may provide a novel mechanism for receptor signaling regulation in cells. The functional coupling between neighboring receptors could improve the signaling performance. The ryanodine receptors (RyR)/calcium release channels usually form 2-D regular lattice in the endoplasmic/sarcoplasmic reticulum membranes. Thus, RyR is a potentially good model to study the function of receptor 2-D array. In this article, we briefly review recent progresses in this research field, including RyR-RyR interaction, RyR array's function and working mechanisms. The investigations performed by new methods in our laboratory are summarized. We demonstrate that the RyR-RyR interaction is modulated by the functional states of RyRs. Accordingly, the mechanism of "dynamic coupling" of RyR array is proposed. Its possible role in RyR-mediated Ca(2+) release is discussed.

Effect of intermittent and continuous hypoxia on ryanodine receptors of rat heart.

Intermittent hypoxia (IH) adaptation has been shown to exert beneficial effects on the functions of hearts that had been subjected to insult by ischemia or ischemia/reperfusion. To understand whether calcium release channels/ryanodine receptors (RyRs) were involved, the effects of IH and continuous hypoxia (CH) on [3H]ryanodine binding to homogenates of rat hearts were investigated. Similar studies were performed on rat skeletal muscle. The main results on cardiac muscle were as follows: 1) Ischemia for up to 45 min in normal rat hearts had no obvious effect on the equilibrium ryanodine binding constant (K(d)), while the maximum number of ryanodine binding sites (B(max)) was affected in a time-dependent manner. B(max) was significantly increased with 15 min ischemia, which then returned to control levels upon prolonging the ischemia to 30 min. After 45 min ischemia, a small decrease of B(max) was observed. 2) IH adaptation for up to 28 days did not change B(max), but a significant decrease of B(max) was apparent after longer IH adaptation or after CH exposure. Although B(max) was not altered by 30 min ischemia, 30 min reperfusion following 30 min ischemia induced an evident decrease of B(max). After either IH or CH adaptation, the ischemia/reperfusion- induced decrease of B(max) was abolished. 3) Several effects on K(d) of ischemia and ischemia/reperfusion, with and without IH or CH adaptation, were observed. The most distinct and consistent finding was that a clear increase of K(d) was induced by ischemia or ischemia/reperfusion in CH adapted rats. [3H]Ryanodine binding to homogenates of rat skeletal muscle was also affected by IH and CH adaptation. In contrast to that found in cardiac muscle, a decrease of B(max) in skeletal muscle appeared only after CH adaptation. The physiological significance of these effects is discussed.

The Accumulation of Diacylglycerol and Activation of Protein Kinase C by Caffeine Treatment in Frog Skeletal Muscle.

Our previous work has shown that high K(+) exposure could induce an accumulation of diacylglycerol (DAG) and the activation of protein kinase C (PKC) in frog skeletal muscle. To elucidate its mechanism, the effect of caffeine on the pathway of DAG/PKC signal transduction was investigated. Caffeine could induce DAG accumulation and PKC activation in a dose- and time-dependent manner. The accumulation of DAG induced by caffeine was significantly different from that produced by high K(+) exposure, although the intracellular calcium was raised to a similar peak. In addition, differences in the activation of PKC were shown between caffeine and high K(+) exposure. These differences suggest that the myoplasmic calcium increase produced by high K(+) exposure is not a sole factor for the activation of DAG/PKC signal transduction in frog skeletal muscle, and the high K(+)-induced depolarization may play some roles.

The Accumulation of Diacylglycerol and Activation of Protein Kinase C Induced by High K(+) Exposure in the Frog Skeletal Muscle.

The effects of high K(+) exposure on the accumulation of diacylglycerol (DAG) and on the activation of protein kinase C (PKC) have been studied in frog skeletal muscle. The endogenous DAG increased by treatment with 80 mM K(+) for different lengths of time. Correspondingly, high K(+) exposure could induce a translocation of PKC. For instance, The membrane-associated PKC activity (pmol/min.g muscle) was increased from the control value of 523mmplus;37 to 725mmplus;33 and 858mmplus;59 after 80 mM K(+) exposure for 2 and 60 minutes, while the cytosolic PKC activity was reduced from 543mmplus;35 to 307mmplus; mmplus;20 and 254mmplus;46, respectively. The accumulation of DAG and the activation of PKC induced by high K(+) exposure suggest a possible role of the pathway of DAG/PKC in the regulation of the excitation-contraction coupling in skeletal muscle fibres.

Proteomic analyses reveal high expression of decorin and endoplasmin (HSP90B1) are associated with breast cancer metastasis and decreased survival.

BACKGROUND: Breast cancer is the most common malignancy among women worldwide in terms of incidence and mortality. About 10% of North American women will be diagnosed with breast cancer during their lifetime and 20% of those will die of the disease. Breast cancer is a heterogeneous disease and biomarkers able to correctly classify patients into prognostic groups are needed to better tailor treatment options and improve outcomes. One powerful method used for biomarker discovery is sample screening with mass spectrometry, as it allows direct comparison of protein expression between normal and pathological states. The purpose of this study was to use a systematic and objective method to identify biomarkers with possible prognostic value in breast cancer patients, particularly in identifying cases most likely to have lymph node metastasis and to validate their prognostic ability using breast cancer tissue microarrays. METHODS AND FINDINGS: Differential proteomic analyses were employed to identify candidate biomarkers in primary breast cancer patients. These analyses identified decorin (DCN) and endoplasmin (HSP90B1) which play important roles regulating the tumour microenvironment and in pathways related to tumorigenesis. This study indicates that high expression of Decorin is associated with lymph node metastasis (p<0.001), higher number of positive lymph nodes (p<0.0001) and worse overall survival (p = 0.01). High expression of HSP90B1 is associated with distant metastasis (p<0.0001) and decreased overall survival (p<0.0001) these patients also appear to benefit significantly from hormonal treatment. CONCLUSIONS: Using quantitative proteomic profiling of primary breast cancers, two new promising prognostic and predictive markers were found to identify patients with worse survival. In addition HSP90B1 appears to identify a group of patients with distant metastasis with otherwise good prognostic features.

Biphasic modulation of ryanodine receptors by sulfhydryl oxidation in rat ventricular myocytes.

To understand better the modulation of ryanodine receptors (RyRs) during oxidative stress, the effect of 4,4'-dithiodipyridine (DTDP), a cell-permeant and thiol-reactive oxidant, on global Ca(2+) signal and spontaneous Ca(2+) sparks of rat ventricular myocytes was investigated. It was shown that a brief Ca(2+) transient was elicited by DTDP, when its concentration was raised to 100 microM DTDP. In addition a dose-dependent increase of cytoplasmic free Zn(2+) concentration was induced by DTDP. An increase of the frequency of spontaneous Ca(2+) sparks appeared at 3 microM DTDP, whereas higher concentration of DTDP caused a biphasic change of the frequency in both intact and permeabilized myocytes. Consistent with the biphasic effect, caffeine-induced Ca(2+) transients were similarly affected. Because DTDP did not reduce the free Ca(2+) concentration in the sarcoplasmic reticulum lumen, it is likely that the effects of DTDP on the frequency and caffeine-induced Ca(2+) transients are due mainly to sulfhydryl oxidation-induced activation and subsequent inactivation of RyRs. Unlike the frequency, the spatio-temporal properties of Ca(2+) sparks were not influenced by DTDP. The finding that DTDP does not affect the duration of Ca(2+) sparks is inconsistent with that the DTDP-induced increase of the open time of reconstituted RyR channels. The mechanism underlying this discrepancy, especially the possible role of the interaction between arrayed RyRs in myocytes, is discussed. This study suggests that, even if oxidative stress is mild enough not to cause intracellular Ca(2+) accumulation, it may affect signaling pathways through directly modulating the RyR or its complex and in turn changing the frequency of spontaneous Ca(2+) sparks. Thus, the functional importance of moderate oxidative stress should not be overlooked.

Effect of osmotic stress on spontaneous calcium sparks in rat ventricular myocytes.

AIM: To study whether the volume of cardiomyocytes and their functions would change under severe pathological conditions or osmotic stress. To clarify the role of ryanodine receptors/calcium release channels (RyRs) in the functional change, the effect of osmotic stress on spontaneous Ca2+ sparks in rat ventricular myocytes was investigated. METHODS: A laser scanning confocal microscope was used to detect spontaneous Ca2+ sparks of intact or saponin permeabilized myocytes loaded with Fluo-4. High and low tonicity was obtained by adding sucrose and reducing NaCl concentration in the external medium, respectively. RESULTS: In intact myocytes the frequency of Ca2+ sparks was increased and decreased by hyperosmotic (1.5 T) and hyposmotic (0.6 T) exposure, respectively. In addition, hyperosmotic exposure increased the temporal parameters and decreased the spatial parameter of Ca2+ sparks, while opposite changes occurred with hyposmotic exposure. The spatio-temporal properties of Ca2+ sparks were slightly affected by altering [K+]i (50-200 mmol/L) in saponin permeabilized myocytes in the presence of 8% dextran. It was observed that the spatio-temporal parameters of the Ca2+ sparks in permeabilized myocytes were dose-dependently altered by dextran. The propagating velocity of Ca2+ waves in intact and permeabilized myocyte was also affected by osmotic pressure or dextran. CONCLUSION: The effect of osmotic stress on the frequency of spontaneous Ca2+ sparks might be ascribed to the change of myoplasmic Ca2+ and Ca2+ content in the sarcoplasmic reticulum, while the effect on the spatio-temporal properties is caused by the alteration of Ca2+ diffusion mainly resulting from the morphological change of the myocytes.

Depletion of FKBP does not affect the interaction between isolated ryanodine receptors.

The ryanodine receptors/calcium release channels (RyRs) usually form two dimensional regular lattices in the endoplasmic/sarcoplasmic reticulum membranes. The native RyR is associated with many auxiliary proteins, including FKBP. It has been indicated that FKBP may play a role in the intermolecular interaction and coupled gating of neighboring RyRs. However, a more recent study shows that FKBP12 is not involved in the physical linkage between neighboring RyR1s. In the present work, the effect of FKBP12 on the interaction between RyR1s isolated from rabbit skeletal muscle was investigated in an aqueous medium with photon correlation spectroscopy. We found that the depletion of FKBP12 did not affect the oligomerization of RyR1s in the medium containing different [KCl] or under different channel functional states. No evidence is obtained for the involvement of FKBP12 in the intermolecular interaction between RyR1s.

Modulation of the oligomerization of isolated ryanodine receptors by their functional states.

The calcium release channels/ryanodine receptors (RyRs) usually form two-dimensional regular lattices in the endoplasmic/sarcoplasmic reticulum membranes. However, the function and modulation of the interaction between neighboring RyRs are still unknown. Here, with an in vitro aqueous system, we demonstrate that the interaction between RyRs isolated from skeletal muscle (RyR1s) is modulated by their functional states by using photon correlation spectroscopy and [(3)H]ryanodine binding assay. High level of oligomerization is observed for resting closed RyR1s with nanomolar Ca(2+) in solution. Activation of RyR1s by micromolar Ca(2+) or/and millimolar AMP leads to the de-oligomerization of RyR1s. The oligomerization of RyR1s remains at high level when RyR1s are stabilized at closed state by Mg(2+). The modulation of RyR1-RyR1 interaction by the functional state is also observed under near-physiological conditions, suggesting that the interaction between arrayed RyR1s would be dynamically modulated during excitation-contraction coupling. These findings provide exciting new information to understand the function and operating mechanism of RyR arrays.

Effect of Zn2+ ions on ryanodine binding to sarcoplasmic reticulum of striated muscles in the presence of pyrithione.

AIM: To explore whether the differential effects of Zn2+ on ryanodine binding to the sarcoplasmic reticulum (SR) of skeletal and cardiac muscles resulted from different permeability of the SR to Zn2+. METHODS: [3H]ryanodine binding assays were performed to examine the effect of Zn2+ on ryanodine binding to the SR in the presence of pyrithione sodium (PyNa), a specific Zn2+ ionophore. RESULTS: As a control, PyNa up to 50 micromol/L did not induce any effect on ryanodine binding to the SR of cardiac muscle. But PyNa 1-100 micromol/L increased ryanodine binding in skeletal muscle with maximum binding (222.2+/-20.9 % of the control) and inhibited ryanodine binding to 50 % of the control at about 500 micromol/L. In the presence of PyNa 10 and 50 micromol/L the dose-dependence of the effect of Zn2+ in cardiac muscle was still monophasic and not changed by PyNa, while the biphasic effect of Zn2+ in skeletal muscle became monophasic. CONCLUSION: Different permeability of the SR to Zn2+ may account for the differential effects of Zn2+ on ryanodine binding in skeletal and cardiac muscles. PyNa is not a strictly specific Zn2+ ionophore.

Effect of zinc ions on caffeine-induced contracture in vascular smooth muscle and skeletal muscle of rat.

The effect of zinc ions on caffeine-induced contracture in vascular smooth muscle and skeletal muscle of rat was studied. In aortic strips, caffeine contracture was depressed by Zn2+ in a dose-dependent manner. Moreover, the extent of the depression of caffeine contracture in the Zn2+ loaded smooth muscle increased with repetitive caffeine exposures. For instance, in the preparations perfused with a medium containing 100 microM [Zn2+] for 15 or 30 min, the first caffeine contractures were similarly depressed to about 60% of the control. However, the subsequent caffeine exposure at 15 min interval could not evoke any contracture. In this study this feature is referred to as activation dependence of the Zn2+ effect. In small bundles of soleus muscle 2ñ100 microM [Zn2+] similarly caused a depression of caffeine contracture, and the activation dependence also was evident. However, an evident potentiation of caffeine contracture was seen in the preparations loaded with lower [Zn2+] such as 0.5 microM, indicating that the effect of Zn2+ on caffeine contracture of skeletal muscle was somewhat different from that seen in smooth muscle. By observing how the depression effect depends on the intervals between caffeine exposures as well as on caffeine concentrations, it is indicated that the activation dependence of the Zn2+ effect, at least in skeletal muscle, may not be explained by depletion of intracellular Ca2+ stores alone. The possible mechanism for that caffeine contracture of smooth muscle and skeletal muscle was differentially affected by Zn2+ ions is discussed.

Modulation of the interactions of isolated ryanodine receptors of rabbit skeletal muscle by Na+ and K+.

Ryanodine receptors (RyRs) of skeletal muscle, as calcium release channels, have been found to form semicrystalline arrays in the membrane of sarcoplasmic reticulum. Recently, both experimental observations and theoretical simulations suggested cooperative coupling within interlocking RyRs. To better understand the interactions between RyRs and their modulation, the aggregation and dissociation of isolated RyRs in aqueous medium containing various Na(+) and K(+) concentrations were investigated using photon correlation spectroscopy (PCS) and atomic force microscopy (AFM). RyRs aggregated readily at low salt concentrations. However, a different behavior was observed in the presence of Na(+) or K(+). Detectable aggregates were formed in 5 microg/mL RyR sample when the concentration of Na(+) and K(+) was reduced from 1 M to below 0.28 and 0.23 M, respectively. The dissociation of RyR aggregates was also examined when raising the salt concentration. While aggregates formed in 0.15 M NaCl medium could reverse almost completely, those formed in 0.15 M KCl medium only dissolved partly. When keeping the total salt concentration at 0.15 M, the aggregation and dissociation of RyRs were seen to evidently depend on the relative concentration of Na(+) and K(+). The interaction between RyRs was strengthened with increasing Na(+)/K(+) ratios in the mixed medium. Accompanying this, a decrease of [(3)H]ryanodine binding occurred. The results obtained with PCS and AFM provide further evidence for the interaction between RyRs and suggest the importance of Na(+), K(+), and their relative composition in modulating the interaction and cooperation between RyRs in vivo.