I wish to study binding induced folding in intrinsically disordered proteins during protein interactions using molecular dynamics. I am considering TIP3P water model and Particle Mesh Ewald (PME) settin in AMBER for long-range electrostatic interactions. However, there is a confusion with regard to the time scale for the simulation and whether i should increase the temperature to observe the conformational changes. Since not much work has been done with respect to IDPs, i would appreciate if someone could suggest or forward relevant literature for designing an effective protocol for the simulation
The best method for this problem may be (well-tempered) metadynamics, which needs some knowledge about both your system and the method itself.
A simpler and less powerful method is replica-exchange.
There are a lot of introductions to these methods freely available on the internet.
Dear Manan,
We are using pDMD (developed by Nikolay Dokholyan) to map structural ensembles of IDPs, it works very well for it. We also used this method to simulate the formation and dissociation of complexes involving IDPs, it seems very reliable. The method is rather fast, easy to use, free for academic use (as far as I know). It has a built-in replica exchange mode, you should use it for these kind of simulations. Attached two pubmed links.
http://www.ncbi.nlm.nih.gov/pubmed/22280505
http://www.ncbi.nlm.nih.gov/pubmed/24763499
TIP3P for water... hmmm... then how do you plan to describe the water-protein H-bonding with these waters? It is essentially temperature-dependent... We have recently published a paper on how water affects IDP conformations (https://www.researchgate.net/publication/274094192_Solvent_Effects_in_the_Helix-Coil_Transition_Model_and_the_Unusual_Biophysics_of_Intrinsically_Disordered_Proteins)
It is tricky to find a good simulational model for water-biopolymer systems. Welcome to the club and good luck!
Article Solvent Effects in the Helix-Coil Transition Model and the U...
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