The tilting motion of the central core reveals the transport mechanism of the sarco/endoplasmic reticulum Ca2+-ATPase.

The sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions per ATP hydrolyzed from the cytoplasm to the lumen. However, how the ATP hydrolysis remotely drives the Ca2+ transport is unclear. In the SERCA1a crystal structures, the ATP hydrolysis is accompanied by the notably increasing tilting angle of the central core (CC) and the Ca2+ transport, and the CC tilting angle dramatically decreases in the E2 to E1 transition. We demonstrated that the significantly increasing tilting motion of the CC drove the Ca2+ release in the molecular dynamics simulation of the R836A variant, and the dramatic spontaneous decrease in the CC tilting angle of the E2 state triggers the restart of the SERCA1a's transport cycle. The repulsion between the phosphorylated D351 and the phosphate groups in ADP triggers the release of ADP from the SERCA1a headpiece. We proposed a novel SERCA transport mechanism in which ATP hydrolysis drives a significant tilting motion of the CC, which drives Ca2+ transport and the A domain rotational motion in the E1P-ADP-2Ca2+ to E2P transition. The dramatic spontaneous decrease in the CC tilting angle of the E2 state drives the restart of the transport cycle.

Treatment of nitrogen and phosphorus from sewage tailwater in paddy rice wetlands: concept and environmental benefits.

Domestic sewage tailwater (DSTW) reuse for crop irrigation is considered a promising practice to reduce water demand, mitigate water pollution, and substitute chemical fertilization. The level of the above environmental benefits of this water reuse strategy, especially when applied to paddy wetlands, remains unclear. In this study, soil column experiments were conducted to investigate the nitrogen and phosphorus fate in paddy wetlands subjected to different tailwater irrigation and drainage strategies, specifically, (i) TW1 and TW2 for regular or enhanced irrigation-drainage without N fertilization, (ii) TW3 and TW4 for regular irrigation with base or tillering N fertilizer, (iii) conventional fertilization N210, and (iv) no-fertilization controls N0. The results showed that the total nitrogen (TN), nitrate (NO3-), and total phosphorus (TP) removal rates from the paddies irrigated by DSTW ranged between 51.92 and 59.34%, 68.1 and 83.42%, and 85.69 and 86.98% respectively. Ammonia emissions from the DSTW-irrigated treatments were reduced by 14.6~47.2% compared to those paddies subjected to conventional fertilization (N210), similarly for TN emissions, with the exception of the TW2 treatment. Overall, it is established that the paddy wetland could effectively remove residual N and P from surface water runoffs, while the partial substitution of chemical fertilization by DSTW could be confirmed. The outcome of this study demonstrates that DSTW irrigation is a promising strategy for sustainable rice production with a minimized environmental impact.

Pharmacophore Oriented MP2 Characterization of Charge Distribution for Anti-SARS-CoV-2 Inhibitor Nirmatrelvir.

Quantum mechanical second order Møller-Plesset (MP2) perturbation theory and density functional theory (DFT) Becke, 3-parameter, Lee-Yang-Parr (B3LYP) and Minnesota 2006 local functional (M06L) calculations were performed to optimize structure of nirmatrelvir and compute the Merz-Kollman electrostatic potential (MK ESP), natural population analysis (NPA), Hirshfeld, charge model 5 (CM5), and mulliken partial charges. The mulliken partial charge distribution of nirmatrelvir exhibits a poor correlation with the MK ESP charges in MP2, B3LYP, and M06L calculations respectively. The NPA, Hirshfeld, and CM5 partial charge scheme of nirmatrelvir indicate a reasonable correlation with MK ESP charge assignments in B3LYP and M06L calculations. The above correlations were not improved by the inclusion of implicit solvation model. The MK ESP and CM5 partial charges show a strong correlation between the results of MP2 and two DFT methods. The three optimized structures present a certain degree of differences from the crystal bioactive conformation of nirmatrelvir, suggesting the nirmatrelvir-enzyme complex is formed in the induced-fit model. The Reactivity of warhead electrophilic nitrile is justified by the relatively weaker strength of π bonds in the MP2 calculations. The nirmatrelvir hydrogen bond acceptors consistently show strong delocalization of lone pair electrons in three calculations, whereas hydrogen bond donors are found to have high polarization on the heavy nitrogen atoms in MP2 computations. This work helps to parametrize the force field of nirmatrelvir and improve accuracy of molecular docking and rational inhibitor design.

QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin.

Intermolecular interaction between key residue N501 of the epitope on SARS-CoV-2 RBD and screening antibody B38 was studied using the QM/MM and QM approach. The QM/MM optimized geometry shows that angle X-H---Y is 165° for O-H---O between mAb light chain S30 and RBD N501. High level MP2 calculations indicated the interaction between RBD N501 and S30 of B38 Fab light chain provide a relatively strong attractive force of - 3.32 kcal/mol, whereas the hydrogen bond between RBD Q498 and S30 was quantified as 0.10 kcal/mol. The decrease in ESP partial charge on hydrogen atom of hydroxyl group on S30 drops from 0.38 a.u. to 0.31 a.u., exhibiting the sharing of 0.07 a.u. from the lone pair electron oxygen of N501 due to hydrogen bond formation. The NBO occupancy of hydrogen atom also decreases from 25.79 % to 22.93 % in the hydroxyl H-O NBO bond of S30. However, the minor change of NBO hybridization of hydroxyl oxygen of S30 from sp3.00 to sp3.05 implies the rigidity of hydrogen bond tetrahedral geometry in the relative dynamic protein complex. The O-H---O angle is 165° which is close but not exactly linear. The structural requirement for sp3 hybridization of oxygen for hydroxyl group on S30 and dimension of protein likely prevent O-H---O from adopting linear geometry. The hydrogen bond strengths were also calculated using a variety of DFT methods, and the result of - 3.33 kcal/mol from the M06L method is the closest to that of the MP2 calculation. Results of this work may aid in the COVID-19 vaccine and drug screening.

New cofactors and inhibitors for a DNA-cleaving DNAzyme: superoxide anion and hydrogen peroxide mediated an oxidative cleavage process.

Herein, we investigated the effects of new cofactors and inhibitors on an oxidative cleavage of DNA catalysis, known as a pistol-like DNAzyme (PLDz), to discuss its catalytic mechanism. PLDz performed its catalytic activity in the presence of ascorbic acid (AA), in which Cu2+ promoted, whereas Fe2+ significantly inhibited the catalytic function. Since Fe2+/AA-generated hydroxyl radicals are efficient on DNA damage, implying that oxidative cleavage of PLDz had no relation with hydroxyl radical. Subsequently, we used Fe2+/H2O2 and Cu2+/H2O2 to identify the role of hydroxyl radicals in PLDz catalysis. Data showed that PLDz lost its activity with Fe2+/H2O2, but exhibited significant cleavage with Cu2+/H2O2. Because Fe2+/H2O2 and Cu2+/H2O2 are popular reagents to generate hydroxyl radicals and the latter also produces superoxide anions, we excluded the possibility that hydroxyl radical participated in oxidative cleavage and confirmed that superoxide anion was involved in PLDz catalysis. Moreover, pyrogallol, riboflavin and hypoxanthine/xanthine oxidase with superoxide anion and hydrogen peroxide generation also induced self-cleavage of PLDz, where catalase inhibited but superoxide dismutase promoted the catalysis, suggesting that hydrogen peroxide played an essential role in PLDz catalysis. Therefore, we proposed a catalytic mechanism of PLDz in which superoxide anion and hydrogen peroxide mediated an oxidative cleavage process.

Probiotic applications of two dominant gut Bacillus strains with antagonistic activity improved the growth performance and immune responses of grouper Epinephelus coioides.

The effect of dietary administration of Bacillus pumilus and Bacillus clausii, the dominant bacteria with antagonistic activity in the gut of fast growing fish, on the growth performance and immune responses of grouper Epinephelus coioides were assessed. The fish were fed for 60 days with three different diets: control (without probiotics), diet T1 supplemented with 1.0x10(8) cells g(-1) B. pumilus, diet T2 with 1.0x10(8) cells g(-1) B. clausii. No significant improvements of weight gain or specific growth rate were observed in the probiotic fed groups, but a significant improvement of feed conversion ratio was observed after 60 days of feeding. Phagocytic activity and phagocytic index of fish fed probiotic diets were significantly higher than those of fish fed the control diet for 60 days. Superoxide dismutase (SOD) concentrations showed no significant difference between the treatments and the control during the whole experiment period, but which increased by 11.4% and 18.5% after 60 days of fed with diets T1 and T2, respectively. The serum lysozyme activities of fish fed diets T1 and T2 were significantly higher than that of fish fed control diet, and had respectively increased by 34.7% and 17.4% compared to the control after 60 days of feeding. Serum complement C3 levels of the treatments were significantly higher than that of control after 30 days of feeding, but no significant difference in serum complement C3 and C4 levels were observed between the treatments and the control after 60 days of feeding. The serum IgM levels of fish fed diet T1 and diet T2 were higher than that of fish fed control diet, and significant increase was observed in fish fed diet T2 for 30 days. The results demonstrated potential for B. pumilus and B. clausii to improve growth performance and immune responses of E. coioides.