I have isolated one compound from plant sources which showed significant inhibition on multiple enzymes of Naja naja venom (Protease, PLA2 and Hyaluronidase). The results are confirmed in both in vitro as well as in vivo experiments.
Further, I want to see the molecular interactions between the compound and the targeted enzyme but unfortunately Naja naja protease and hyaluronidase structures are not available. In this case how do I perform docking studies to get the molecular interaction details?
How could I draw conclusion if I take these enzyme structures from any other venoms?
Any information in this regard is more valuable to me.
you can check the structures in PDB. Particularly the phospholipase structures are well studied. If the homology of the PLA2 that you isolated is very high with the reported structure, you can use it for docking purpose. Secondly you can prepare the model of the enzyme by using swiss model program, and compare it with the reported structures. I hope this would help.
You have not specified which type of the protease you have isolated. Whether a serine or metallo or some other protease.
Dear Aisha,
I have not purified any enzymes from snake venom. I have isolated a plant compound that has inhibitory activity against serine protease, hyaluronidase and PLA2 enzymes of Naja naja crude venom. The results are conformed with multiple experiments. However, I want to see the molecular interactions between the plant compound and enzymes but, protease and hyaluronidase structures are not available for Naja naja venom. As you said, PLA2 is well studied and the structures are available so I dont have problem with PLA2. Here the problem is structure of protease and hyaluronidase. Kindly help me in this regard.
Yours Sincerely
Gopi
I guess this is not the way of working. You must first partially fractionate the venom. Then check the inhibitory activity. The peak in which you are able to identify Hyaluronidase and serine protease, do the SDS page, and then do the identification of the proteins by doing the mass spectrometric analysis of the tryptic digest of the bands you see on the SDS page. In this way you will get information about the sequence. Once you have the sequence of the protein , it will be easier for you to do further work. I hope this would help you.
If your target is not exist in rcsb.org, you can model it by the flowing methods:
1) homology modeling
2) threading
3) prediction based on quantum mechanic.
for homology modeling, you need to have the target sequence deposited in swiss prot database. then, you have to BLAST your sequence and find the best template with the solved 3D structure. sequence similarity above 40% could be suitable. finally, you can model it by numerous software. one of the famous software, which is free for academic, is MODELLER.
GOOD LUCK
Hi,
If you want to proceed with your work then homology modeling will be suitable for you.There are many web server and software available for this work such as I-TASSER, Swiss model, phyre 2 etc. and as a standalone software MODELLER is best as mentioned by Sako Mirzaie . you can also view the List of protein structure prediction software and for docking Autodock is good.
Best of luck
zhanglab.ccmb.med.umich.edu/I-TASSER/
www.sbg.bio.ic.ac.uk/phyre2/
en.wikipedia.org/wiki/List_of_protein_structure_prediction_software
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