Project ID: IPD6520

Project Title: Elusive elapid: Biogeographic venom variation in Indian kraits and its repercussion on snakebite therapy

Principal Investigator: Dr. Kartik Sunagar

PI Affiliation: Assistant Professor, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, Karnataka, India.

Description: Snakebite is a major public health concern in many parts of the world, including India, where over 58,000 deaths occur annually due to this highly neglected tropical disease. The common krait (Bungarus caeruleus), one of the ‘big four’ Indian snakes, is responsible for the second-highest number of snakebite-related deaths in the country. The venom protein composition of common krait venoms from different locations were investigated. Venoms were pre-fractionated using RP-HPLC and SDS-PAGE, and subjected to mass spectromentry analysis. The relative abundance of each toxin family was estimated and compared across different locations.

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Sample Preparation: The venoms were fractionated on a Shimadzu LC-20AD series HPLC system (Kyoto, Japan). A total of 1 mg of venoms were reconstituted in water and injected into a reversed-phase C18 Shim-Pack GIST column [4.6 x 250 mm, 5 μm particle size and 100 Å pore size (Shimadzu, Japan)]. The fractions were eluted at a flow rate of 1 mL/min under following gradient of buffer A (0.1% TFA in HPLC grade water), buffer B (0.1% TFA in acetonitrile) : 5% B for 5 min, followed by 5–15% B for 10 min, 15–45% B for 60 min, and 45–70% B for 10 min and held at 70% r B for 9 min, followed by 70-98% B for 6 min and again held at 98% B for 5 min and completed with 5% B for 5 min. Fractions were collected separately by monitoring the absorbance peaks at 215 nm. A combined analysis strategy was adopted for mass spectrometry, wherein RP-HPLC fractions with higher peak area were subjected to reducing SDS-PAGE and smaller peaks that could not be visualised on the gel were directly subjected to in-solution digestion. The excised gel bands were destained using 30% acetonitrile in 50 mM ammonium bicarbonate buffer. The gel pieces were dehydrated using 100% acetonitrile, followed by reduction using 10 mM dithiothreitol (DTT) at 56 °C for 45 min and alkylation using 55 mM iodoacetamide for 35 min at room temperature.

Peptide Separation: The samples were then digested using sequencing-grade trypsin and incubated overnight at 37 °C. The following day, the supernatant was collected and desalted in a Pierce C18 spin column (Thermofisher Scientific, USA) following the manufacturer’s protocol before being subjected to mass spectrometric analyses. Similarly, for in-solution digestion, fractions were reduced and alkylated using DTT (100 mM) and iodoacetamide (100 mM), respectively, followed by tryptic digestion. The digested peptides were subjected to nano-Liquid Chromatography (nano-LC) and electrospray ionisation tandem mass spectrometry (ESI-MS/MS). The samples were injected into a PepMap C18 nano-LC column (50 cm x 75 μm, 2 μm particle size and 100 Å pore size) mounted on the Thermo EASY nLC Ultimate 3000 series system (Thermo Fisher Scientific, MA, USA), following a gradient elution of buffer A (0.1% formic acid in MS grade water) and buffer B (0.1% formic acid in 80% acetonitrile) at a constant flow rate of 250 nL/min for 90 min. An 8-35% gradient of buffer B was used over the first 70 min for elution, followed by 35 - 95% over the next 5 min, and finally 95% for the last 15 min. The following protocol was adopted to perform the MS scans: scan range (m/z) of 300 - 2000 with a resolution of 120000 and maximum injection time of 100 ms. To perform the precursor (MS) and fragment (MS/MS) scans, an orbitrap detector with high collision dissociation (HCD) fragmentation (30%) was used with the following parameters: scan range (m/z) of 110 –2000 and maximum injection time of 50 ms.

Protein Characterization: Raw MS/MS spectra were searched against the National Center for Biotechnology Information non-redundant (NCBI-NR) Serpentes database (taxid: 8570) to identify toxins that constitute the venom fractions. The search was performed in PEAKS Studio X Plus software (Bioinformatics Solutions Inc., ON, Canada) by setting parent and fragment mass error tolerance limits to 10 ppm and 0.6 Da, respectively. A ‘monoisotopic’ precursor ion search type and semispecific trypsin digestion were specified as parameters. Fixed and variable modifications were set as carbamidomethylation (+57.02) and oxidation (+14.99), respectively. The False Discovery Rate (FDR) was set to 0.1%, and PEAKS Studio automatically determined the corresponding -10lgP cutoff value. Hits with at least one unique matching peptide were considered for protein identification, and redundant hits from each protein family were manually removed.

Experiment Type: Bottom-up

PubMed-ID:

Species: Bungarus caeruleus-132961

Tissue: Venom gland (bto:0001440)

Cell Type:

Disease: Unknown

Instrument Details: Orbitrap Fusion (MS:1002416)

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