-deltaG(AB) and pH dependence of the electron transfer from P(+)Q(A)(-)Q(B) toP(+)Q(A)Q(B)(-) in Rhodobacter sphaeroides reaction centers

The electron transfer from the reduced primary quinone (Q(A)(-)) to the secondary quinone (Q(B)) can occur in two phases with a well-characterized 100 micros component (tau(2)) and a faster process occurring in less than 10 micros (tau(1)). The fast reaction is clearly seen when the native ubiquinone-10 at Q(A) is replaced with naphthoquinones. The dependence of tau(1) on the free-energy difference between the P(+)Q(A)(-)Q(B) and P(+)Q(A)Q(B)(-) states (-) and on the pH was measured using naphthoquinones with different electrochemical midpoint potentials as Q(A) in Rhodobacter sphaeroides reaction centers (RCs) and in RCs where - is changed by mutation of M265 in the Q(A) site from Ile to Thr (M265IT). Q(B) was ubiquinone (UQ(B)) in all cases. Electron transfer was measured by using the absorption differences of the naphthosemiquinone at Q(A) and the ubisemiquinone at Q(B) between 390 and 500 nm. As - was changed from -90 to -250 meV tau(1) decreased from 29 to 0.2 micros. The free-energy dependence of tau(1) provides a reorganization energy of 850 +/- 100 meV for the electron transfer from Q(A)(-) to Q(B). The slower reaction at tau(2) is free-energy independent, so processes other than electron transfer determine the observed rate. The fraction of the reaction at tau(1) increases with increasing driving force and is 100% of the reaction when - is approximately 100 meV more favorable than in the native RCs with ubiquinone as Q(A). The fast phase, tau(1), is pH independent from pH 6 to 11 while tau(2) slows above pH 9. As the Q(A) isoprene tail length is increased from 2 to 10 isoprene units the fraction at tau(1) decreases. However, tau(1), tau(2), and the fraction of the reaction in each phase are independent of the tail length of UQ(B).     

Errors in power-law estimations of inflow rates for intracranial aneurysm CFD

Patient-specific inflow rates are rarely available for computational fluid dynamics (CFD) studies of intracranial aneurysms. Instead, inflow rates are often estimated from parent artery diameters via power laws, i.e. Q ∝ Dⁿ, reflecting adaptation of conduit arteries to demanded flow. The present study aimed to validate the accuracy of these power laws. Internal carotid artery (ICA) flow rates were measured from 25 ICA aneurysm patients via 2D phase contrast MRI. ICA diameters, derived from 3D segmentation of rotational angiograms, were used to estimate inflow rates via power laws from the aneurysm CFD literature assuming the same inlet wall shear stress (WSS) (n = 3), velocity (n = 2) or flow rate (n = 0) for all cases. To illustrate the potential impact of errors in flow rate estimates, pulsatile CFD was carried out for four cases having large errors for at least one power law. Flow rates estimated by n = 3 and n = 0 power laws had significant (p < 0.01) mean biases of −22% to +32%, respectively, but with individual errors ranging from −78% to +120%. The n = 2 power law had no significant bias, but had non-negligible individual errors of −58% to +71%. CFD showed similarly large errors for time-averaged sac WSS; however, these were reduced after normalizing by parent artery WSS. High frequency WSS fluctuations, evident in 2/4 aneurysms, were also sensitive to inflow rate errors. Care should therefore be exercised in the interpretation of aneurysm CFD studies that rely on power law estimates of inflow rates, especially if absolute (vs. normalized) WSS, or WSS instabilities, are of interest.     

Reproducibility of the multiple inert gas elimination technique

Although measurement errors in the multiple inert gas elimination technique have a coefficient of variation of approximately 3%, small biological fluctuations in ventilation, blood flow, or other variables must contribute additional variance to this method of assessing ventilation-perfusion (VA/Q) mismatch. To determine overall variance of computed indices of VA/Q mismatch, an analysis of variance was carried out using a total of 400 duplicate pairs of inert gas samples obtained from canine (N = 118) and human (N = 282) studies in the past 2 years. In both sets VA/Q mismatch ranged from minimal (2nd moment of ventilation and blood flow distributions, log SDV and log SDQ, respectively approximately equal to 0.3 each) to severe (log SDV and log SDQ approximately equal to 2.0). Differences between duplicate log SD values were computed and found to be a constant fraction of the mean log SD of each duplicate pair, averaging 13% for both canine and human ventilation and blood flow data. The resultant coefficient of variation for a single measurement of log SD about its mean averaged 8.6% for all data combined. This analysis demonstrates excellent reproducibility of these dispersion indices over a wide range of conditions, and if the mean of duplicate values is used, thus reducing variability by square root 2 to 6.1%, log SD can be estimated with an approximately 95% confidence limit of +/- 12%.     

Electrogenic Protonation of the Secondary Quinone Acceptor Q<Subscript>B</Subscript> in Spinach Photosystem II Complexes Incorporated into Lipid Vesicles

The generation of transmembrane electric potential difference (delta psi) in quinone acceptor complex of proteoliposomes containing core complexes of photosystem II from spinach was studied using for the measurements a direct electrometric technique. Besides the fast increase in the membrane potential associated with the electron transfer between the redox-active tyrosine 161 residue (Y(Z)) in D1 polypeptide and the primary quinone acceptor Q(A), an additional electrogenic phase with tau approximately 0.85 msec at pH 7.3 and the maximal relative amplitude of approximately 11% of the Y(Z)ox Q(A)- phase was observed after the second light flash. The sensitivity of this phase to diuron (an inhibitor of electron transfer between Q(A) and the secondary quinone acceptor Q(B)), the dependence of its amplitude on the light flash parity, and also a decrease in its rate constant with increase in pH indicated that it was due to dismutation of Q(A)- and Q(B)- with the subsequent protonation of a doubly reduced plastoquinone molecule: Q(A)- Q(B)- + 2H+ --> Q(A)Q(B)H2.     

Determination of the benztropine analog AHN-1055, a dopamine uptake inhibitor, in rat plasma and brain by high-performance liquid chromatography with ultraviolet absorbance detection

N-Substituted 3alpha-[bis(4'-fluorophenyl)methoxy] tropanes represent a series of novel potential cocaine abuse therapeutics. AHN-1055, a member of this series, has been assessed to be the most suitable analog for pharmacokinetic studies. A sensitive and specific high-performance liquid chromatography method was developed to quantitate AHN-1055 in rat plasma and brain tissue. Reversed-phase chromatography with ultraviolet detection (lambda=220 nm) was utilized to quantitate the eluate. Plasma or brain tissue samples were prepared by liquid-liquid extraction using hexane, followed by evaporation, reconstitution in mobile phase, and injection onto an ABZ+plus column. AHN-1055 and oxprenolol (internal standard) eluted at approximately 9.9 and 5.01 min, respectively, without any interfering peaks. The calibration curves were found to be linear in the range of 25-10000 ng/ml for plasma and 50-5000 ng/g for brain (r2> or =0.999). The intra- and inter-day variabilities were < or =10% whereas the intra- and inter-day errors were < or =8.5%. Plasma and brain recoveries of AHN-1055 were 95 and 79%, respectively. Stability studies showed plasma quality control samples to be stable through at least three freeze-thaw cycles (error<3.5%), for at least 24 h when subjected to room temperature (error<3%) and for at least 30 h after loading the processed samples onto the autosampler (error<3%). AHN-1055 stock solution was found to be stable for at least 4 months when stored at 4 degrees C (error<6%). The validated method accurately quantified AHN-1055 in plasma and brain samples collected from a pharmacokinetic study consisting of an intravenous bolus in the tail vein of adult male Sprague-Dawley rats.     

Observation of the protonated semiquinone intermediate in isolated reaction centers from Rhodobacter sphaeroides: implications for the mechanism of electron and proton transfer in proteins.

A proton-activated electron transfer (PAET) mechanism, involving a protonated semiquinone intermediate state, had been proposed for the electron-transfer reaction k(2)AB [Q(A)(-)(*)Q(B)(-)(*) + H(+) <--> Q(A)(-)(*)(Q(B)H)(*) --> Q(A)(Q(B)H)(-)] in reaction centers (RCs) from Rhodobacter sphaeroides [Graige, M. S., Paddock, M. L., Bruce, M. L., Feher, G., and Okamura, M. Y. (1996) J. Am. Chem. Soc. 118, 9005-9016]. Confirmation of this mechanism by observing the protonated semiquinone (Q(B)H)(*) had not been possible, presumably because of its low pK(a). By replacing the native Q(10) in the Q(B) site with rhodoquinone (RQ), which has a higher pK(a), we were able to observe the (Q(B)H)(*) state. The pH dependence of the semiquinone optical spectrum gave a pK(a) = 7.3 +/- 0.2. At pH < pK(a), the observed rate for the reaction was constant and attributed to the intrinsic electron-transfer rate from Q(A)(-)(*) to the protonated semiquinone (i.e., k(2)AB = k(ET)(RQ) = 2 x 10(4) s(-)(1)). The rate decreased at pH > pK(a) as predicted by the PAET mechanism in which fast reversible proton transfer precedes rate-limiting electron transfer. Consequently, near pH 7, the proton-transfer rate k(H) > 10(4) s(-)(1). Applying the two step mechanism to RCs containing native Q(10) and taking into account the change in redox potential, we find reasonable values for the fraction of (Q(B)H)(*) congruent with 0.1% (consistent with a pK(a)(Q(10)) of approximately 4.5) and k(ET)(Q(10)) congruent with 10(6) s(-)(1). These results confirm the PAET mechanism in RCs with RQ and give strong support that this mechanism is active in RCs with Q(10) as well.     

The effect of dibenzo[a,1]pyrene and benzo[a]pyrene on human diploid lung fibroblasts: the induction of DNA adducts, expression of p53 and p21(WAF1) proteins and cell cycle distribution

Polycyclic aromatic hydrocarbons (PAHs) present in ambient air are considered as potential human carcinogens, but the detailed mechanism of action is still unknown. Our aim was to study the in vitro effect of exposure to dibenzo[a,l]pyrene (DB[a,l]P), the most potent carcinogenic PAH ever tested, and benzo[a]pyrene (B[a]P) in a normal human diploid lung fibroblast cells (HEL) using multiple endpoints. DNA adduct levels were measured by 32P-postlabelling, the expression of p53 and p21(WAF1) proteins by western blotting and the cell cycle distribution by flow cytometry. For both PAHs, the DNA adduct formation was proportional to the time of exposure and dependent on the stage of cell growth in culture. DNA binding was detectable even at the lowest concentration used (24h exposure, 0.01 microM for both PAHs). The highest DNA adduct levels were observed after 24h of exposure in near-confluent cells (>90% of cells at G0/G1 phase), but DNA damage induced by DB[a,l]P was approximately 8-10 times higher at a concentration one order of magnitude lower as compared with B[a]P (for B[a]P at 1 microM and for DB[a,l]P at 0.1 microM: 237+/-107 and 2360+/-798 adducts/10(8) nucleotides, respectively). The induction of p53 and p21(WAF1) protein occurred subsequent to the induction of DNA adducts. The DNA adduct levels correlated with both p53 (R=0.832, P<0.001 and R=0.859, P<0.001, for DB[a,l]P and B[a]P, respectively) and p21(WAF1) levels (R=0.808, P<0.001 and R=0.797, P=0.001, for DB[a,l]P and B[a]P, respectively), regardless of the PAH exposure and the phase of cell growth. The results showed that a detectable increase of p53 and p21(WAF1) proteins (> or = 1.5-fold as compared with controls) requires a minimal DNA adduct level of approximately 200-250 adducts/10(8) nucleotides for both PAHs tested and suggest that the level of adducts rather than their structure triggers the p53 and p21(WAF1) responses. The cell cycle was altered after 12-16h of treatment, and after 24h of exposure to 0.1 microM DB[a,l]P in growing cells, there was approximately 24% increase in S phase cells accompanied by a decrease in G1 and G2/mitosis (G2/M) cells. Cell treatment with 1.0 microM B[a]P resulted in more subtle alterations. We conclude that DB[a,l]P, and to a lesser degree B[a]P, are able to induce DNA adducts as well as p53 and p21(WAF1) without eliciting G1 or G2/M arrests but rather an S phase delay/arrest. Whether the S phase delay observed in our study is beneficial for the survival of the cells remains to be further established.     

Identification of the proton pathway in bacterial reaction centers: decrease of proton transfer rate by mutation of surface histidines at H126 and H128 and chemical rescue by imidazole identifies the initial proton donors.

The pathway for proton transfer to Q(B) was studied in the reaction center (RC) from Rhodobacter sphaeroides. The binding of Zn(2+) or Cd(2+) to the RC surface at His-H126, His-H128, and Asp-H124 inhibits the rate of proton transfer to Q(B), suggesting that the His may be important for proton transfer [Paddock, M. L., Graige, M. S., Feher, G. and Okamura, M. Y. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 6183-6188]. To assess directly the role of the histidines, mutant RCs were constructed in which either one or both His were replaced with Ala. In the single His mutant RCs, no significant effects were observed. In contrast, in the double mutant RC at pH 8.5, the observed rates of proton uptake associated with both the first and the second proton-coupled electron-transfer reactions k(AB)(()(1)()) [Q(A)(-)(*)Q(B)-Glu(-) + H(+) --> Q(A)(-)(*)Q(B)-GluH --> Q(A)Q(B)(-)(*)-GluH] and k(AB)(()(2)()) [Q(A)(-)(*)Q(B)(-)(*) + H(+) --> Q(A)(-)(*)(Q(B)H)(*) --> Q(A)(Q(B)H)(-)], were found to be slowed by factors of approximately 10 and approximately 4, respectively. Evidence that the observed changes in the double mutant RC are due to a reduction in the proton-transfer rate constants are provided by the observations: (i) k(AB)(1) at pH approximately pK(a) of GluH became biphasic, indicating that proton transfer is slower than electron transfer and (ii) k(AB)(2) became independent of the driving force for electron transfer, indicating that proton transfer is the rate-limiting step. These changes were overcome by the addition of exogenous imidazole which acts as a proton donor in place of the imidazole groups of His that were removed in the double mutant RC. Thus, we conclude that His-H126 and His-H128 facilitate proton transfer into the RC, acting as RC-bound proton donors at the entrance of the proton-transfer pathways.     

Interactions between the donor and acceptor sides in bacterial reaction centers

The apparent equilibrium constant K'(2) for electron transfer between the primary (Q(A)) and secondary (Q(B)) quinone acceptors of the reaction center was measured in chromatophores of Rhodobacter capsulatus. In the presence of the oxidized primary donor P(+), we obtained a value of K'(2)(P(+)) approximately 100 at pH 7.2, based on the rates of recombination from P(+)Q(A-) and P(+)Q(B-). K'(2) was also measured in the presence of reduced P, from the damping of semiquinone oscillations during a series of single turnover flashes. A 5-fold smaller value, K'(2)(P) approximately 20, was found. Additional information on the interactions between the donor and acceptor sides was obtained by measuring the shift of the midpoint potential of P caused by the presence of Q(B-) or Q(A-)S (where S indicates the presence of the inhibitor stigmatellin). A stabilization of the oxidized state P(+) was observed in both instances, by 10 mV for Q(B-) and 30 mV for Q(A-)S. The larger stabilization of P(+)Q(A-)S with respect to P(+)Q(B-) does not account for the effect of P(+)/P on K'(2). Analysis of these results indicates that the interactions between P(+)/P and Q(A)/Q(A)(-) are markedly modified depending on the occupancy of the Q(B) pocket by ubiquinone or by stigmatellin. We propose that the large value of K'(2)(P(+)) results essentially from a conformational destabilization of the P(+)Q(A-) state, that is relieved when the proximal site of the Q(B) pocket is occupied by stigmatellin.     

Substitution-rate variation among sites and the estimation of transition bias

Substitution-rate variation among sites and differences in the probabilities of change among the four nucleotides are conflated in DNA sequence comparisons. When variation in rate exists among sites but is ignored, biases in the rates of change among nucleotides are underestimated. This paper provides a quantification of this effect when the observed proportions of transitions, P, and transversions, Q, between two sequences are used to estimate transition bias. The utility of P/Q as an estimator is examined both with and without rate variation among sites. A gamma-distributed-rates model is used to illustrate the effect that variation among sites has on estimates of transition bias, but it is argued that the basic results should hold for any pattern of rate variation. Naive estimates of the extent of transition bias, those that ignore rate variation when it is present, can seriously underestimate its true value. The extent of this underestimation increases with the amount of rate variation among sites. An example using human mitochondrial DNA shows that a simple comparison of the proportions of transitions and transversions in recently diverged sequences underestimates the level of transition bias by approximately 15%. This does not depend on the use of P/Q to estimate transition bias; maximum-likelihood methods give similar results.      

Quantification of regional V/Q ratios in humans by use of PET. I. Theory

With positron emission tomography, quantitative measurements of regional alveolar and mixed venous concentrations of positron-emitting radioisotopes can be made within a transaxial section through the thorax. This allows the calculation of regional ventilation-to-perfusion (V/Q) ratios by use of established tracer dilution theory and the constant intravenous infusion of 13N. This paper considers the effect of the inspiration of dead-space gas on regional V/Q and investigates the relationship between the measured V/Q, physiological V/Q, and V/Q defined conventionally in terms of bulk gas flow (VA/Q). Ventilation has been described in terms of net gas transport, and the term effective ventilation has been introduced. A simple two-compartment model has been constructed to allow for the reinspiration of regional (or personal) and common dead-space gas. By use of this model, with parameters representative of normal lung the effective V/Q ratio for 13N [(VA/Q)eff(13N)] is shown to overestimate VA/Q by 18% when VA/Q = 0.1 but underestimate VA/Q by 68% when VA/Q = 10. For physiological gases, the model predicts that the behavior of O2 should be similar to that of 13N, so that, in terms of gas transport, V/Q ratios obtained using the infusion of 13N closely follow those for O2. Values of the effective V/Q ratio for CO2 [(VA/Q)eff(CO2)] lie approximately halfway between (VA/Q)eff(13N) and VA/Q. These results indicate that dead-space ventilation is far less a confounding issue when V/Q is considered in terms of net gas transport (VAeff), rather than bulk flow (VA).(ABSTRACT TRUNCATED AT 250 WORDS)     

Charge stabilization in reaction center protein investigated by optical heterodyne detected transient grating spectroscopy

Photosynthetic reaction center (RC) pigment protein complex converts the free energy of light into chemical potential of charge pairs with extremely high efficiency. A transient phase in the absorption spectrum in the sub-millisecond time scale is expected to be especially important to examine the conformational gating model of the Q (A) (-) Q(B) to Q(A)Q (B) (-) (here Q(A )and Q(B) are the primary and secondary quinone type electron acceptors, respectively) electron transport. Essential kinetic components at few tens of microseconds scale and at around 200 mus have been suggested. We investigated the conformation change of RCs using heterodyne detection of the laser-induced transient grating method. An about 25 mus dynamics was observed, which coincides with the one described by the conformational gating model and possibly related to the nonadiabatic intrinsic Q (A) (-) Q(B) to Q(A)Q (B) (-) electron transport. The relative intensity of this component decreased with increasing quinone concentration indicating an initial (P(+)Q (A) (-) )(1) or a relaxed (P(+)Q (A) (-) )(2 )conformational substate. We did not find the decay component at few hundreds of microseconds time scale indicating that there is no large displacement in the RC structure if Q(B) is present. The diffusion coefficient of the RC/LDAO detergent micelles calculated from the kinetic component was D = 3.8 x 10(-11 )m(2)/s that agrees fairly well with the number estimated from the Einstein-Stokes relationship, and relates to a hydrodynamic diameter of 11.4 nm of the RC in LDAO micellar solution.     

Determination of the rate and yield of B-side quinone reduction in Rhodobacter capsulatus reaction centers

In the native purple bacterial reaction center (RC), light-driven charge separation utilizes only the A-side cofactors, with the symmetry related B-side inactive. The process is initiated by electron transfer from the excited primary donor (P*) to the A-side bacteriopheophytin (P* --> P+ H(A)-) in approximately 3 ps. This is followed by electron transfer to the A-side quinone (P+ H(A)- --> P+ Q(A)-) in approximately 200 ps, with an overall quantum yield of approximately 100%. Using nanosecond flash photolysis and RCs from the Rhodobacter capsulatus F(L181)Y/Y(M208)F/L(M212)H mutant (designated YFH), we have probed the decay pathways of the analogous B-side state P+ H(B)-. The rate of the P+ H(B)- --> ground-state charge-recombination process is found to be (3.0 +/- 0.8 ns)(-1), which is much faster than the analogous (10-20 ns)(-1) rate of P+ H(A)- --> ground state. The rate of P+ H(B)- --> P+ Q(B)- electron transfer is determined to be (3.9 +/- 0.9 ns)(-1), which is about a factor of 20 slower than the analogous A-side process P+ H(A)- --> P+ Q(A)-. The yield of P+ H(B)- --> P+ Q(B)- electron-transfer calculated from these rate constants is 44%. This value, when combined with the known 30% yield of P+ H(B)- from P in YFH RCs, gives an overall yield of 13% for B-side charge separation P* --> P+ H(B)- --> P+ Q(B)- in this mutant. We determine essentially the same value (15%) by comparing the P-bleaching amplitude at approximately 1 ms in YFH and wild-type RCs.     

Reactions between primary and secondary acceptors of photosystem II in Chlorella pyrenoidosa under anaerobic conditions as studied by chlorophyll fluorescence.

The kinetics of the fluorescence yield phi of chlorophyll a in Chlorella pyrenoidosa were studied under anaerobic conditions in the time range from 50 mus to several minutes after short (t 1/2 = 30 ns or 5 mus) saturating flashes. The fluorescence yield "in the dark" increased from phi = 1 at the beginning to phi approximately 5 in about 3 h when single flashes separated by dark intervals of about 3 min were given. After one saturating flash, phi increased to a maximum value (4-5) at 50 mus, then phi decreased to about 3 with a half time of about 10 ms and to the initial value with a half time of about 2 s. When two flashes separated by 0.2 s were given, the first phase of the decrease after the second flash occurred within 2 ms. After one flash given at high initial fluorescence yield, the 10-ms decay was followed by a 10 s increase to the initial value. After the two flashes 0.2 s apart, the rapid decay was not followed by a slow increase. These and other experiments provided additional evidence for and extend an earlier hypothesis concerning the acceptor complex of Photosystem II (Bouges-Bocquet, B. (1973) Biochim. Biophys. Acta 314, 250-256; Velthuys, B. R. and Amesz. J. (1974) Biochim. Biophys. Acta 333, 85-94): reaction center 2 contains an acceptor complex QR consisting of an electron-transferring primary acceptor molecule Q, and a secondary electron acceptor R, which can accept two electrons in succession, but transfers two electrons simultaneously to a molecule of the tertiary acceptor pool, containing plastoquinone (A). Furthermore, the kinetics indicate that 2 reactions centers of System I, excited by a short flash, cooperate directly or indirectly in oxidizing a plastohydroquinone molecule (A2-). If initially all components between photoreaction 1 and 2 are in the reduced state the following sequence of reactions occurs after a flash has oxidised A2- via System I: Q-R2- + A leads to Q-R + A2- leads to QR- + A2-. During anaerobiosis two slow reactions manifest themselves: the reduction of R (and A) within 1 s, presumably by an endogenous electron donor D1, and the reduction of Q in about 10 s when R is in the state R- and A in the state A2-. An endogenous electron donor, D2, and Q- complete in reducing the photooxidized donor complex of System II in reactions with half times of the order of 1 s.     

Coenzyme Q10, carotenoid,tocopherol, and retinol levels in cord plasma from multiethnic subjects in Hawaii

Abstract

Coenzyme Q10 (Q10), carotenoids, tocopherols, and retinol are the major circulating lipid-phase micronutrients (LPM) known to help mitigate oxidative damage and prevent chronic diseases. However, the functions of these compounds in newborns are little understood. This is due, in part, to the paucity of studies reporting their concentrations in this population.

We measured Q10, carotenoids, tocopherols, and retinol in cord plasma from 100 multiethnic subjects living in Hawaii using HPLC with diode array and electrochemical detection. Appropriate internal standards were used including, for the first time, custom designed oxidized (UN10) and reduced (UL10) Q10 analogues. These compounds reflected the oxidation of UL10 to UN10 that occurred during sample processing and analysis and thus permitted accurate adjustments of natively circulating Q10 levels.

All LPM measured were much lower in cord than in peripheral plasma. Cord plasma levels of total carotenoids, tocopherols, and retinol were approximately 10-fold, 3- to 5-fold and 1.5- to 3-fold lower than those in children or women. Cord plasma levels of total Q10 (TQ10; median, 113 ng/mL) were approximately 2-fold or 7- to 9-fold lower than peripheral plasma levels of neonates or children and adults, respectively. In contrast, the UN10/TQ10 ratio was substantially higher in cord (24%) than in peripheral plasma of children (3–4%) or adults (9%). Among the 5 ethnic groups in our cohort, no differences were observed in the levels of UN10, UL10, or TQ10. However, significant differences in many of the LPM were observed between ethnicities. More research is needed to explain these phenomena.     

Monte Carlo estimation of the number of possible protein folds: effects of sampling bias and folds distributions

The estimation of the number of protein folds in nature is a matter of considerable interest. In this study, a Monte Carlo method employing the broken stick model is used to assign a given number of proteins into a given number of folds. Subsequently, random, integer, non-repeating numbers are generated in order to simulate the process of fold discovery. With this conceptual framework at hand, the effects of two factors upon the fold identification process were investigated: (1) the nature of folds distributions and (2) preferential sampling bias of previously identified folds. Depending on the type of distribution, dividing 100,000 proteins into 1,000 folds resulted in 10-30% of the folds having 10 proteins or less per fold, approximately 10% of the folds having 10-20 proteins per fold, 31-45% having 20-100 proteins per fold, and >30% of the folds having more than 100 proteins per fold. After randomly sampling one tenth of the proteins, 68-96% of the folds were identified. These percentages depend both on folds distribution and biased/non-biased sampling. Only upon increasing the sampling bias for previously identified folds to 1,000, did the model result in a reduction of the number of proteins identified by an order of magnitude (approximately 9%). Thus, assuming the structures of one tenth of the population of proteins in nature have been solved, the results of the Monte Carlo simulation are more consistent with recent lower estimates of the number of folds, 相似文献   

Oxidation of the non-heme iron complex in photosystem II

In photosystem II (PSII), the redox properties of the non-heme iron complex (Fe complex) are sensitive to the redox state of quinones (Q(A/)(B)), which may relate to the electron/proton transfer. We calculated the redox potentials for one-electron oxidation of the Fe complex in PSII [E(m)(Fe)] based on the reference value E(m)(Fe) = +400 mV at pH 7 in the Q(A)(0)Q(B)(0) state, considering the protein environment in atomic detail and the associated changes in protonation pattern. Our model yields the pH dependence of E(m)(Fe) with -60 mV/pH as observed in experimental redox titration. We observed significant deprotonation at D1-Glu244 in the hydrophilic loop region upon Fe complex oxidation. The calculated pK(a) value for D1-Glu244 depends on the Fe complex redox state, yielding a pK(a) of 7.5 and 5.5 for Fe(2+) and Fe(3+), respectively. To account for the pH dependence of E(m)(Fe), a model involving not only D1-Glu244 but also the other titratable residues (five Glu in the D-de loops and six basic residues near the Fe complex) seems to be needed, implying the existence of a network of residues serving as an internal proton reservoir. Reduction of Q(A/B) yields +302 mV and +268 mV for E(m)(Fe) in the Q(A)(-)Q(B)(0) and Q(A)(0)Q(B)(-) states, respectively. Upon formation of the Q(A)(0)Q(B)(-) state, D1-His252 becomes protonated. Forming Fe(3+)Q(B)H(2) by a proton-coupled electron transfer process from the initial state Fe(2+)Q(B)(-) results in deprotonation of D1-His252. The two EPR signals observed at g = 1.82 and g = 1.9 in the Fe(2+)Q(A)(-) state of PSII may be attributed to D1-His252 with variable and fixed protonation, respectively.     

Effects of random and non-random errors on phenotypic selection in autotetraploids

Summary A theoretical investigation was made to ascertain the effects of random and non-random deviations, called errors, of phenotypic from genotypic values on population means and on the response to phenotypic recurrent selection. The study was motivated as a selection experiment for disease resistance where there was either variability in the inoculation or environment (the random errors) or where the inoculation was above or below the the optimum rate where genetic differences in resistance are maximized (the non-random errors). The study was limited to the genetics at a diallelic locus (alleles B and b) in an autotetraploid population in random mating equilibrium. The response to selection was measured as the covariance of selection and compared to the exact covariance which was the covariance of selection without errors in phenotype. The random errors were modeled by assuming that a given percentage () of the population was uniformly distributed among the five possible genotype classes independent of their true genotypes. This model was analyzed numerically for a theoretical population with the frequency of the B allele (p) ranging from 0.0 to 1.0 and assumed errors of=0.1 and 0.5 for the following six types of genic action of the B allele: additive, monoplex dominance, partial monoplex dominance, duplex dominance, partial duplex dominance, and recessive. The effect of random error was to consistently reduce the response to selection by a percentage independent of the type of genic action at the locus. The effect on the population mean was an upward bias when p was low and a downward bias when p approached unity. In the non-random error model below optimum inoculations altered the phenotypes by systematically including percentage of susceptible genotypes into one or more other genotype classes with more genetic resistance (a positive shift). With above optimum inoculations, some resistant genotypes are classed with the non-resistant genotypes (a negative shift). The effects on the covariance of selection were found by numerical analysis for the same types of genic action and's as investigated for random error. With a negative shift and a low p, the covariance of selection was always reduced, but for an increasing p the covariance approached and exceeded the exact covariance for all types of genic action except additive. With a positive shift and a low p, response to selection was greatly improved for three types of genic action: duplex dominance, partial duplex dominance, and recessive. The effect of a non-random error on population means was to greatly bias the means upwards for a low p and positive shift, but with increasing p the bias decreased. A relatively slight decrease in the mean occurred with a negative shift. This study indicated check varieties commonly used to monitor selection pressures in screening programs are very responsive to positive non-random shifts, but are relatively unresponsive to negative shifts. The interaction of selection pressure, types of genic action, and genotypes in the class shift models was suggested as a partial explanation for the lack of response to increasing selection pressures observed in some breeding programs.Cooperative investigations of the Alfalfa Production Research Unit, United States Department of Agriculture, Agricultural Research Service, and the Nevada Agricultural Experiment Station, Reno, Nevada. Paper No. 404 Scientific Journal Series. Nevada Agricultural Experiment Station     

Electrostatic role of the non-heme iron complex in bacterial photosynthetic reaction center

To elucidate the role of the non-heme iron complex (Fe-complex) in the electron transfer (ET) events of bacterial photosynthetic reaction centers (bRC), we calculated redox potentials of primary/secondary quinones Q(A/B) (E(m)(Q(A/B))) in the Fe-depleted bRC. Removing the Fe-complex, the calculated E(m)(Q(A/B)) are downshifted by approximately 220 mV/ approximately 80 mV explaining both the 15-fold decrease in ET rate from bacteriopheophytin (H(A)(-)) to Q(A) and triplet state occurrence in Fe-depleted bRC. The larger downshift in E(m)(Q(A)) relative to E(m)(Q(B)) increases the driving-energy for ET from Q(A) to Q(B) by 140 meV, in agreement with approximately 100 meV increase derived from kinetic studies.