Mechanism of Substrate Translocation by a Ring-Shaped ATPase Motor at Millisecond Resolution

Ring-shaped, hexameric ATPase motors fulfill key functions in cellular processes, such as genome replication, transcription, or protein degradation, by translocating a long substrate through their central pore powered by ATP hydrolysis. Despite intense research efforts, the atomic-level mechanism transmitting chemical energy from hydrolysis into mechanical force that translocates the substrate is still unclear. Here we employ all-atom molecular dynamics simulations combined with advanced path sampling techniques and milestoning analysis to characterize how mRNA substrate is translocated by an exemplary homohexameric motor, the transcription termination factor Rho. We find that the release of hydrolysis product (ADP + Pi) triggers the force-generating process of Rho through a 0.1 millisecond-long conformational transition, the time scale seen also in experiment. The calculated free energy profiles and kinetics show that Rho unidirectionally translocates the single-stranded RNA substrate via a population shift of the conformational states of Rho; upon hydrolysis product release, the most favorable conformation shifts from the pretranslocation state to the post-translocation state. Via two previously unidentified intermediate states, the RNA chain is seen to be pulled by six K326 side chains, whose motions are induced by highly coordinated relative translation and rotation of Rho’s six subunits. The present study not only reveals in new detail the mechanism employed by ring-shaped ATPase motors, for example the use of loosely bound and tightly bound hydrolysis reactant and product states to coordinate motor action, but also provides an effective approach to identify allosteric sites of multimeric enzymes in general

Determination of Chiral Jasmonates in Flowers by GC/MS after Monolithic Material Sorptive Extraction

A GC/MS method with monolithic material sorptive extraction (MMSE) pretreatment was developed to determine contents of the enantiomers of jasmonic acid and methyl jasmonate in flowers. To optimize MMSE extraction, several MMSE parameters were investigated, including extraction temperature, extraction time, and extraction solvent. Under the optimal conditions, extraction efficiency was good. Using the selected-ion monitoring mode, the limit of detection (LOD, <i>S</i>/<i>N</i> = 3) for methyl jasmonates was 0.257 ng/mL. The limit of quantitation (LOQ, <i>S</i>/<i>N</i> = 10) was 0.856 ng/mL. The linearity range was 1–100 ng/mL. The average recovery of methyl jasmonate at lower concentration was 116.8% (2 ng/mL). The relative standard deviation of methyl jasmonate contents determined within the linear range of detection was less than or equal to 15% of the mean determined level. The proposed method is rapid, sensitive, and competently applied to the determination of jasmonic acid and methyl jasmonate enantiomers in flowers

Additional file 1: of Efficacy and safety of electroacupuncture for post stroke depression: study protocol for a randomized controlled trial

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HRMS identification data of purified tannins.

<p>HRMS identification data of purified tannins.</p

Examples of MS/MS fragments of purified dimeric, trimeric, tetrameric and pentameric PA.

<p>Examples of MS/MS fragments of purified dimeric, trimeric, tetrameric and pentameric PA.</p

Quantification of Arachidonic Acid and Its Metabolites in Rat Tissues by UHPLC-MS/MS: Application for the Identification of Potential Biomarkers of Benign Prostatic Hyperplasia

<div><p>To evaluate the potential relationship between benign prostatic hyperplasia (BPH) and the arachidonic acid (AA) metabolome, a UHPLC—MS/MS method has been developed and validated for simultaneous determination of AA and its cyclooxygenase(COX) and lipoxygenase(LOX) pathway metabolites (15-HETE, 12-HETE, TXA₂, 5-HETE, AA, PGI₂, PGF_2α, 8-HETE, PGD₂, PGE₂ and LTB₄) in rat tissues. The analytes were extracted from tissue samples with a protein precipitation procedure and then separated on a Shim-pack XR-ODSC18 column with 0.05% formic acid in water (pH adjusted with dilute ammonia) and methanol:acetonitrile (20:80, v/v). Detection was performed on a UHPLC—MS/MS system with electrospray negative ionization (ESI) and a multiple reaction-monitoring mode. The lower limits of quantification (LLOQ) were 0.25–50 ng/mL for all of the analytes in the prostate, seminal, bladder, liver and kidney tissues. The absolute recoveries of the analytes from all of the tissues were more than 50%. By means of the method developed, the AA metabolites in tissue samples from Sham and BPH group rats were determined. The eleven biomarkers in the BPH group prostate, seminal, bladder, liver and kidney tissues were significantly higher than those of the sham group, indicating that BPH fortified the inducible expression of COX and LOX, as well as increased the production of AA and eicosanoids. The method described here offers a useful tool for the evaluation of complex regulatory eicosanoids responses in vivo.</p></div

sj-docx-1-taj-10.1177_20406223221122478 – Supplemental material for Association of NAFLD with cardiovascular disease and all-cause mortality: a large-scale prospective cohort study based on UK Biobank

Supplemental material, sj-docx-1-taj-10.1177_20406223221122478 for Association of NAFLD with cardiovascular disease and all-cause mortality: a large-scale prospective cohort study based on UK Biobank by Wen Ma, Wentao Wu, Weixing Wen, Fengshuo Xu, Didi Han, Jun Lyu and Yuli Huang in Therapeutic Advances in Chronic Disease</p

Hematoxylin and eosin staining of prostate ventral lobe (1) and dorsal lobe (2) from sham group rats (A) and BPH induced rats (B).

<p>Hematoxylin and eosin staining of prostate ventral lobe (1) and dorsal lobe (2) from sham group rats (A) and BPH induced rats (B).</p

The histograms of 11 analytes in prostate, bladder, seminal, liver, kidney from BPH group rats (BPH) and sham group rats (sham).

<p>The histograms of 11 analytes in prostate, bladder, seminal, liver, kidney from BPH group rats (BPH) and sham group rats (sham).</p

Concentration of oligomeric tannins in filtrates with/without salivary protein interaction (* indicates “not detected”).

<p>Concentration of oligomeric tannins in filtrates with/without salivary protein interaction (* indicates “not detected”).</p