PROTEIN-DNA and PROTEIN-peptide

User discussions
1

GROMACS version:2019
GROMACS modification: Yes/No
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Hello Everyone!

I want to run MD simulation on protein-peptide and protein-RNA complexes using the charm36 forcefield.

  1. As for the protein-peptide complex, do I need to generate a topology file for the peptide separately (as a ligand) as described in the “protein-ligand complex tutorial” by Prof Justin Lemkul or I should treat the protein-peptide complex as a whole using the pdb2gmx.

  2. I will also like to know how to go about the or things to consider in protein-RNA complex MD simulation.

Regards,

Mukhtar

2
  1. Yes, you can prepare topology file for protein-peptide or protein-dna systems using pdb2gmx command.
  2. Mg+2 ion plays and important role in stability of RNA, DNA systems. So while neutralizing the system you need to consider Mg+2 ions.
    Best,
    Abhijit
    Senior Scientist
    Quantumzyme LLP, Bangalore
3

Thanks for the response. I ran a short MDS using pdb2gmx to generate a topology file for my protein-peptide complex. However, I am faced with more challenges:

  1. please how can i get the RMSD of the peptide relative to protein?
  2. I will also like to do binding energy analysis using the g_mmpbsa tool, how can i generate an index file containing my protein and peptide (as 1 and 13 in the g_mmpbsa tutorial)
4

Hi,

  1. If you do gmx make_ndx then you will see the protein Backbone which consists of both the protein and peptide atoms. Check the atom range of the protein and peptide in .gro file and from there create another index of only Protein-Backbone and Peptide-Backbone. You can do this using the atom range in make_ndx command:
    for example a 1-500
  2. Follow the above procedure to create index file of Protein and Peptide by selecting the atom range.
    Best,
    Abhijit
    Senior Scientist
    Quantumzyme LLP
5

Thanks for the wonderful suggestions.

I will like to bother you, I have run a 50ns MDS on my apoprotein and protein-peptide complex (red), and attached is the result. I used the Group 4 Backbone selection for the RMSD and ROG plot. However, I could only infer that the peptide binding to my protein confers great changes and instability when compared with the apoprotein( black) trajectory.

Couple with this, I also generated index files for my protein-peptide, peptide only, and protein only for MMPBSA calculation. please how can I go about it
Uploading: gy
mmpbsa
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Uploading: mmpbsa.jpg…

gyrate
gyrate792×612 46.7 KB

rmsd
rmsd792×612 46.2 KB

6

Hi,
Can you be more specific? I didn’t understand your question?
Best,

Hi,
Simply RMSD or Rg will not give you proper understanding of stability. To understand the stability, you need to calculate thermodynamic properties which can be calculated from the enhanced sampling techniques, such as metadyamics and umbrella sampling. In this case, you may try protein-peptide contacts with the distance as a collective variable and calculate the free energy plot. You can explore the plumed software for the same.
Best,
Dr Abhijit Kayal
Senior Scientist
Quantumzyme LLP

7

I generated a RMSD and ROG plot from the 50ns MDS I ran for my apoprotein and protein-peptide complex. I made an inference that my protein-peptide deviates a lot and is less stable than the apoprotein (based on the RMSD and ROG plot). I will like to know if my interpretation is correct. Apoprotein (black) protein-peptide (red).

8

okay. I will check it out.

Thanks