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59 protocols using phosphatidylserine

1

Characterization of RyR1 and SERCA1 interactions

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[3H]Ryanodine and 45Ca2+ were purchased from GE-Healthcare (Chicago, IL). Phosphatidylserine, phosphatidylcholine and phosphatidylethanolamine were obtained from Avanti Polar Lipids Inc. (Alabaster, AL). Free-base efavirenz (EFV) was obtained from Shengda Pharmaceutical Co (Zhejiang, China), Atazanavir (ATV) sulfate was purchased from Gyma Laboratories of America, Inc (Westbury, NY). Dialysis membranes were obtained from Spectrum Laboratories Inc (Rancho Dominguez, CA). Mouse monoclonal RyR1 antibodies (34C), mouse monoclonal SERCA1 antibodies (VE121G9) and FKBP12 Monoclonal Antibody (OTI3B3) were obtained from Fisher Scientific (Waltham, Massachusetts). All other reagents and solvents used were of the highest grade commercially available.
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2

Lipid-mediated HIV-1 Inhibitor Interactions

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[3H]Ryanodine was purchased from Perkin-Elmer Health Science Inc (Boston, MA, USA). Phosphatidylserine, phosphatidylcholine, and phosphatidylethanolamine were obtained from Avanti Polar Lipids Inc. (Alabaster, AL, USA). Free-base efavirenz (EFV) and ritonavir (RTV) were obtained from Shengda Pharmaceutical Co (Zhejiang, China), and atazanavir (ATV) sulfate was purchased from Gyma Laboratories of America, Inc (Westbury, NY, USA). Abacavir (ABC), bictegravir (BIC), rilpivirine (RPV), and tenofovir disoproxil fumarate were purchased from Boc Sciences (Shirley, NY, USA). Dialysis membranes were obtained from Spectrum Laboratories Inc (Rancho Dominguez, CA, USA). Recombinant HIV-Tat protein (ab83353) was obtained from Abcam (Waltham, MA, USA). All other reagents and solvents used were of the highest grade commercially available.
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3

Purification and Characterization of His-Tagged Proteins

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n-octyl β-D-glucoside (OG) was purchased from Affymetrix, Inc., Santa Clara, CA. Phosphatidylcholine (chicken egg, PC) and phosphatidylserine (porcine brain, PS) were purchased from Avanti Polar Lipids, Inc., Alabaster, AL. Polyclonal His-tag antibody and anti-rabbit-HRP antibody were purchased from GenScript USA, Inc., Piscataway, NJ. Co-NTA resin was purchased from Thermo Fisher Scientific, Rockford, IL. All other chemicals were purchased from Sigma Aldrich or Thermo Fisher Scientific. Restriction enzymes, DNA polymerases, ligase and markers were purchased from New England Biolabs.
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4

Chromogenic Thrombin Generation Assay

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The thrombin-specific chromogenic substrate Tosyl-Gly-Pro-Arg-p-nitroanilide (Chromozym-TH) was purchased from Sigma (USA).
For the thrombin generation test, the following reagents were used: thrombin-specific fluorogenic substrate Z-Gly-Gly-Arg-AMC (Bachem, Switzerland); 7-amino-4-methylcoumarin, СаСl2, dimethyl sulfoxide (DMSO), and NaCl (Sigma-Aldrich, USA); thromboplastin (Renam, Russia); phosphatidylserine (from pig brain) and phosphatidylcholine (from egg yolk) produced by Avanti Polar Lipids Inc. (USA); and 4-(2-hydroxyethyl)-1-piperazine-2-ethanosulphonic acid (HEPES, Fisher Biotech, USA).
The calibrator for the determination of thrombin activity in the CAT test (ThrCal) was purchased from Thrombinoscope BV (the Netherlands) through Laborama (Russia).
Dabigatran (BIBR 953) was obtained from Selleckhem.com. HC-IOC-019s (C6H5-SO2-O-C6H4(CH3)-O-(CH2)2-NC5H4(NH2)) was synthesized at the Institute of Organic Chemistry of Russian Academy of Sciences (Russia)33 (link). Pradaxa (dabigatran etexilate) (capsules 110 mg) was from Boehringer Ingelheim (Germany).
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5

Reconstitution of RyR2 Channels in Bilayers

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RyR2 channels were incorporated into planar phospholipid bilayers as previously described [23 (link)] in a 1 : 1 mixture of phosphatidylethanolamine : phosphatidylserine (Avanti Lipids). Current fluctuations through RyR2 channels were recorded under voltage-clamp conditions with 250 mM HEPES, 80 mM Tris, 2 µM free Ca2+, pH 7.2, on the cytoplasmic side and 250 mM glutamic acid, 10 mM HEPES, pH to 7.2 with Ca(OH)2 (free [Ca2+] approximately 50 mM) on the trans (luminal) side of the bilayer at 21°C. The luminal chamber was voltage-clamped at ground. The free [Ca2+] and pH of the solutions were measured using a Ca2+ electrode (Orion 93-20, Thermo Fisher Scientific, UK) and a Ross-type pH electrode (Orion 81-55, Thermo Fisher Scientific, UK) as previously described [23 (link)].
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6

Comprehensive Lipidomic Profiling of Kidney

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10 μl of homogenized kidney in 150 mM ammonium bicarbonate (1:20, v/v) were mixed with 490 μl of butanol:methanol (1:1, v/v) spiked with deuterated internal standards (IS). The standards used were acylcarnitine 16:0 D3, cholesterol ester 18:0 D6, ceramide d18:0/08:0, ceramide d18:1/12:0, deoxyceramide m18:1/12:0, cholesterol D7, diacylglycerol 15:0/15:0, GM3 ganglioside d18:1/18:0 D3, monohexosylceramide d18:1/12:0, dihexosylceramide d18:1/12:0, trihexosylceramide d18:1/18:0 D3, lysophosphatidylcholine 13:0, lysophosphatidylethanolamine 14:0, phosphatidylcholine 13:0/13:0, plasmalogen phosphatidylcholine 18:0/18:1 D9, phosphatidylethanolamine 17:0/17:0, plasmalogen phosphatidylethanolamine 18:0/18:1 D9, phosphatidylglycerol 17:0/17:0, phosphatidylinositol 12:0/13:0, phosphatidylserine 17:0/17:0, sphingomyelin d18:1/12:0, sphinganine d17:0, sphingosine d17:1, triacylglycerol 12:0/12:0/12:0 and were purchased from Avanti Lipids. The mixture was vortexed for 2 min, sonicated for 30 min, and then centrifuged twice at 4°C (14,000 g for 10 min). The supernatant fraction was collected for LC-MS/MS analysis. A pooled lipid extract was used as a quality control (QC) sample and injected every 5 study samples.
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7

Purification of Coagulation Factors

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Protein S-free C4BP was purified (29) and APC was activated from in house purified protein C as described (30) (31) (32) . Recombinant FV R506Q/R679Q was expressed and quantified as described (33) , bovine FX (34) and human prothrombin were purified from plasma (35) .
Human α-thrombin was prepared from purified prothrombin (36) . Phospholipids were purchased from Avanti Polar Lipids and include the natural phospholipids phosphatidylserine (PS; brain extract), phosphatidylethanolamine (PE; egg extract) and phosphatidylcholine (PC; egg extract) and the synthetic phospholipids 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-Dioleoyl-sn-glycero-3-phosphoserine (DOPS), and 1,2-Dioleoyl-sn-glycero-3phosphoethanolamine (DOPE). Phospholipid vesicles were prepared by extrusion technique (37) .
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8

Incorporation of KirBac3.1 Proteoliposomes into Planar Lipid Bilayers

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KirBac3.1 proteoliposomes were incorporated into planar lipid bilayers separating two aqueous chambers (cis and trans). Bilayers were produced using the Mueller method 44 . Bilayers were formed across an aperture in a delrin cup with diameter 150-250 µm using a lipid mixture of phosphatidylethanolamine, phosphatidylcholine and phosphatidylserine (7:2:1 wt/wt, Avanti Polar Lipids) in n-decane (50 mg ml -1 , ICN Biomedicals). The cis chamber contained 250 mM KCl and 1.0 mM CaCl2 and the trans chamber contained 50 mM KCl and 0.1 mM CaCl2. Proteoliposomal fusion with bilayers was initiated by adding 5 µl aliquots of the proteoliposome preparation (described above) to the cis bath whilst stirring. During experiments, the composition of the cis solution was altered by a perfusion system 45 that allowed exposure of single channels to additions of spermine or KCl/NaCl substitutions within ~ 1 s. All solutions were pH buffered using 10 mM N-tris[hydroxymethyl] methyl-2aminoethanesulfonic acid (TES; ICN Biomedicals) and titrated to pH 7.4 using KOH (ICN Biomedicals). KCl was obtained from Aldrich and CaCl2 from BDH Chemicals. Experiments were carried out at room temperature (23 ± 2 o C).
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9

Lipidomic Analysis of Spirulina

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Lipid analysis of dry spirulina was performed by Avanti Polar Lipids (Alabaster, AL, USA). Modified Bligh and Dyer extractions (Bligh and Dyer 1959) were performed with EquiSPLASH™ Lipidomix™, and Lipidyzer™ standards (Avanti Polar Lipids), and different chain lengths of phosphatidylglycerol, phosphatidylserine, and phosphatidylinositol (Avanti Polar Lipids) were added as internal standards (IS). Total lipids were dried then resolvated in 1 mL of 1:1 methylene chloride:methanol. Samples were injected in triplicate without dilution for LC-MS analysis. The methodology used was hydrophophilic interaction liquid chromatography (HILIC), which separates lipids into classes and subclasses that span a narrow retention time window (Hines et al. 2017) . A standard of 18:1 cholesterol ester was used as an IS for stigmasterols and brassicasterols. Data are presented as ng/mg of sample. Values were calculated using a point calibration determined by multiplying area ratio averages for the analyte to IS and multiplying by the concentration of IS.
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10

Lipid Standards for Lipidomics

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The lipid standards phosphatidic acid (PA) 16:0/18:1, phosphatidylcholine (PC) 16:0/18:1, phosphatidylethanolamine (PE) 16:0/18:2, phosphatidylinositol (PI) 18:1/16:0, phosphatidylserine (PS) 16:0/18:1 were purchased from Avanti Polar Lipids, Inc. (Alabaster, Alabama, USA). Further reagent and material details are provided in the ESI. †
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