Pankaj Thapa

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Questions related from Pankaj Thapa

How is Phosphatidylcholine (PC)- Phosphatidylethanolamine (PE) ratio calculated? #lipid #analysis #worm #c.elegans #massspec ?

Our aim was to compare the differential activity (if any) for our protein of interest that is involved in lipid metabolism (can be quantified using PC/PE ratio, already shown in mice and human...

24 March 2022 6,791 0 View

How to plot the distribution spectra from the hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) data?

Hi have a protein (X, a dimer) HDX MS data in the presence and absence of ligands/interacting partner. Our interest is to look at the dimeric nature of X, whether it fluctuates or have symmetry to...

05 February 2021 3,520 3 View

How strong a interaction should be there between two proteins to be studied using Gel filtration chromatography?

I am working with two different proteins; which were proven to interact with each other using in vitro pull down, co-ip (both with recombinant proteins and from in-vivo system) studies....

30 March 2019 3,421 6 View

How to solve or make 2D construction maps from negative staining images?

I have managed to get good images from negative staining grids of protein complexes (120 to 230 kDa) which seem homogenous and consistent with regards to the radii as per their molecular weights...

24 October 2018 4,686 2 View

How to model a dimer from a monomer pdb?

Hi, I wish to generate a dimer model of protein X, which I modeled using modeling tool (Swiss model using crystal structure of mouse, has homology ~96%, was solved as a dimer). The modeled...

10 August 2018 5,569 11 View

How to purify protein with pI-5.8, using ion exchange chromatography?

I have a protein with pI-5.8 which has 6xHis tag at its N terminal and is not giving good affinity purification yield. To which i have been suggested to use ion exchange chromatography with the...

28 March 2018 6,506 5 View

What is the acceptable amount of sarkosyl for protein purification?

I am trying to purify a protein involved in DNA repair and is a part of supra-molecular complex. This protein was over-expressed using pET28a construct in BL21 2DE3 cells but its induction was...

12 January 2018 1,223 3 View

Need suggestion for suites or tools for building the model of protein derived from X ray diffration data

I have managed to solve the structure of a protein for which X ray diffraction data was collected and using a template structure, which was only missing 13 amino acids from the N terminal side,...

25 July 2017 8,364 3 View

Is number of ub modification on a protein at specific site (followed by polyubuquitination at k48 or k29) definitive of its degradation

does the conformation of the protein near the site of ubiquitination play any role in deciding the fate of the protein despite having the kiss of death?

04 July 2017 8,273 0 View

List of Breast Cancer associated proteins?

I wish to carry out an exhaustive study of all the proteins which are involved/associated in/with breast cancer (associated directly or indirectly both, with regards to its progression, increase...

16 October 2016 1,825 4 View