i'm working on a plant protein. The aim is to induce a point mutation to block the binding of one of many ligands which bind to the protein in question.
I can then perform experiments done on the native protein (which are well established) during its characterization. This will should show that this specific ligand is important for one of the roles of the protein complex.
That's the general aim of my work and will be great if the theory turns out to be true.
But if so, I would like to show this in vivo by comapring a wild type plant with on with this mutation.
Any ideas or tips where to find some info for rational plant genome modification? Is it at all possible, I'm not really fond of the idea of screening thousands of random mutants from irradiation or ems (will run out of time and funding probably by the time I finish.) The gene is nuclear encoded and might have a couple of copies (or maybe not, I don't remember right now. This was kind of a spontaneous idea )
Part of my PhD involves doing some molecular dynamics between protein pigment containing complexes. I aiming to see how certain pigments within each complex influence the aggregation process under certain conditions.
I have no experience in molecular dynamics, but I'm working through the VMD/NAMD tutorials.
However, I'm not sure, if the I should include the pigments with the proteins when generating segment individual the psf files.
I do know that:
- only 2 of the large number of pigments should be involved in the process I want to analyze
- all of the pigments, except from one of the 2, have structural importance for the folding of the protein
The dynamics will be checked within a lipid membrane.
I hope I've explained the problem in and understandable way.
So, my questions are:
- should I include the pigments with the protein strands in the segments during psf generation
- any advice on finding the best sequence of doing tutorials related to molecular dynamics using NAMD