Hi Markos.
No, we consider only the dynamics of water adsorbed on the protein. We focus on water at different interfaces (hydrophobic and hydrophilic, organic and inorganic, nanostructured and not, soft and hard), including water in channels and pores, but we did not consider, for the moment, ion channels. It is definitely an interesting subject! If you have any reference for it, please share it with us.
Thank you ,
Giancarlo
Hi Giancarlo,
For a review about what i am talking about see:
"Hydrophobic Gating in Ion Channels"
J Mol Biol. 2015 January 16; 427(1): 121–130. doi:10.1016/j.jmb.2014.07.030.
Is something like that of interest for you?
Best,
Markos
From the conclusions of this review it seems that the questions left open are mainly biological, and that the role played by water has been clearly settled down. Is it so?
From a physical point of view, there are still many issues open, e.g. how to model this first-order transition of water vaporizing in the nanopore. From a biological point of view, there is a lot of potential, for drug discovery.
About the vaporization transition in nanopores, we just published results that could help in understanding: Martí, J.; Calero, C.; Franzese, G. Structure and Dynamics of Water at Carbon-Based Interfaces. Entropy 2017, 19, 135. http://www.mdpi.com/1099-4300/19/3/135 (open access). In the last part we show how the vaporization is related to the confinement length. Is this relevant for your point?
Yes, this is relevant. However, is there a similar approach for the pore of protein systems? To the best of my knowledge, not.
No, but it could be done and I guess the results should be similar as long as the protein pore is mainly hydrophobic. Which protein pore would you suggest to consider?
The "protoype" ion channel system that we consider nowadays is the Arcobacter butzleri (NavAb) channel (pdb code: 3RVY). This system is characterized by a wide hydrophobic central cavity (CC), but also by a strongly hydrophilic, and narrow, selectivity filter (SF). Its function is determined by the interplay of hydrophobic and hydrophilic interactions across different spatial scales, as well as, by a locally-dependent pore radius.
- Badges
- Science topic
- Similar topics
- Biological Science
- Bioecology
- Systems Ecology
- Landscape Ecology
- Connectivity