Protocol on how to 3D print protein structures?

Looking for potential collaborators for molecular dynamics related work for some manuscripts. Authorship and credits will be given, Please let us know

I have performed 200ns simulation of the protein ligand complex using Schrodinger Desmond .

My story is that I want to predict that my ligand causes the conformational change and dissociate or destabilize the chains of protein .

My protein has two chains A and B in total 805 amino acids , I have docked the compound on site as mentioned per literature it shows -5.9 to -7.2kcal per mol docking score on site as mentioned in literature

Then I make a complex of best pose on ligand , what I want to discuss that I want that binding of ligand on chain A doesn't effect on stability of protein but binding of ligand on chain B or at Interface could produce the big chain on conformation of protein as well as stability and dissociate them .

That I want , the ligand as proved such mechanism in invitro studies.

I am attaching the results the RMSD of protein and ligand was stable in begining but suddenly it hits up 50A.

The question is that if the protein rmsd is so high so it could create effect on ligand Rmsd or not and if ligand rmsd is high and I want instability so it would be acceptable or not .

I have performed the apo system simulation also it shows Rmsd less than 4A and fluctuations are less .

In comparison with ligand the system was highly unstable .

So how I will present my results because most simulation are done to check stability but here I want instability of protein protein Interaction after ligand attachment to chain B to any part of it or at Interface even reaching to chain

I have also calculated the distance of main amino acids needed for stabilization of protein there distance also increase very much .and fluctuations are more also .

In conclusion I want instability in protein after ligand attachment .

Kindly discuss in detail any one with generous comments.

Thanks .

I am trying to insert cholesterol inside the DPPC membrane by using gmx insert_molecules -replace. But number of DPPC molecules replaced is much higher than the number of cholesterol inserted? Please suggest me a way to build the system by replacing desired number of DPPC.

In the molecular dynamics simulation analysis part, how to calculate molecular surface area (MolSA) and polar surface area (PSA) in gromacs ?

I'm currently doing an experiment where I'm following the expression of a reporter gene (GFP) along growth using S. cerevisiae. The cultivations last around 48 hours. I observed that the results from run to run are very reproducible, in terms of trend/curve shape. However, I cannot say the same regarding the fluorescence values. For the calculations, I subtract the GFP autofluorescence with the correspondent non-GFP expressing strain, and then normalize according to O.D. The settings of the microplate reader are also the same (same gain function, etc). However, even maintaining all the parameters, I get, in terms of number values, different results from run to run (for instance, for the same strain, in one run the fluorescence values normalized are 20000 for one run, and 12000 for another run, althought the curve has precisely the same shape from run to run). I guess that this means that I need a kind of a standart that I know the fluorescence will be the same from run to run, and always need to normalize the GFP values from cells according to that standart. But what should I use?

Thank you!

I am running docking by using Autodock 4.2 software. However, I am not able to run autodock at the final stage and this type of command error appears in the terminal,

Unknown ligand atom type "atotypin"; add parameters for it to the parameter library first!

Autodock 4.2 runs without errors for similar ligands but this error is seen with ligands having Br and Cl groups.

I edited the autodock parameters tool, But still I faced current problem

So I was running an RT-qPCR, but as you can see from the attachment some of my technical replicate triplets have CT values that vary by 1 (e.g. 26.16, 25.88, 25.14), leading to standard deviation greater than 0.5.

What to do then? Can I still keep the good results and re-run the problem ones on a new plate with the same housekeeping gene? I have made aliquots of the same samples and primers that I can use.

Also, any advice on how to prevent CT value variation in replicates. This is probably a pipetting error, right? As an inexperienced undergrad I spent 3 hours making this plate ;(

Hi all,

I would like to improve IgG denaturation in my sample before running an SDS-PAGE. I have seen papers where 4 to 8M Urea is added in the sample.

Can anyone tell me if this concentration corresponds to the final concentration after mixing with loading buffer?

How would you prepare your sample technically and what is the stock solution of Urea to prepare?

Thanks a lot for your input!

Mariette