Hello Everyone, I want to use NAMD to simulate transemembrane protein with copper as a ligand. Can anyone guide me how to fix the following issues;
1. Do I need to dock copper to my protein first? If yes then will that be appropriate because I guess docking can not give us the expected binding conformation of Copper with Histadine residue. I am interested in a conformation as observed in crystal structure, 2SOD (pdb id).
2. Which force field will be more appropriate? I am used to use CHARMM27 but for normal proteins.
Thanks to all of you in advance.
Dear Ashfaq Ahmed,
I am writing few sentence that might be useful for you . In fact , I have no information about NAMD but usually I am using another package for In- Silico drug design . In your case you have a target (transemembrane protein) and Ligand (copper), First thing you have to modify your protein file like removing water molecules and determine active site ( pocket) in you protein. Then you have to modify the ligand like minimize its energy, finally you can go to docking experiment. and analyse your data.
Kindly write again for more discussion
Thank you
Afshaq,
You need not DOCK the copper ions in your protein. You can just INSERT it into your protein. Its simple task in spdbv. You just need to load protein and copper ions separately in two layers and later on merge these two layers in one single layer. There you go... your copper ions are inserted in right place. If you find difficulty doing this you can mail me your protein and zinc ions. I will do it for you.
The second task involving NAMD is a bit tricky because I am not sure the forcefield file you are using contains parameters for copper ions. Moreover you shall also need the topology for copper ions if they are coordinated to neighboring amino acid residues. So my advice on this matter for you is to first find topology (if coppers are coordinated) and parameter for copper ion and then use it.
Any one out there who know where to find parameters for copper ions? This question has increased my curiosity.
Thanks @Rohan and Abaas: I have already successfully simulated ATP, ADP etc with protein but this time Cu is giving me an immense challenge and trouble. Still I am trying to find a way because i almost finish google search but almost zero specific hits. Further I have some wet lab data which is very very promising about CusS, (Copper Sensor). The protein i am dealing is actually a model with a periplasmic domain and two TMHs. So We are not sure exactly where to keep Cu that is why i preferred docking. Second, the periplasmic part has many His and Met residues but after obtaining a model i can figure out 1 pocket to which I can call active pocket where Trp, His and Met can potentially surround Cu. But the real issue is still finding of topology file.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics