Hello,
A change in allocation has been requested:
Requester: roux (Benoit Roux)
Project: kcsa
Title: Computational study of ion selectivity in the KcsA channel
Description: Understanding quantitatively the microscopic factors controlling ion selectivity remains a great challenge. In simple terms, the concept of selectivity means that the "correct" ion, is able to binding more favorably than an "incorrect" ion. At a physical level, it is to be anticipated that energetics and solvation play a key role in this process, although different aspects of energetics may be highlighted by the various experimental methods used to probe the system. Some experimental measurements are more sensitive to the relative depth of free energy wells, while others are more sensitive to the relative height of free energy barriers. In the case of ion channels, the large hydration energy of the ions contrasts with the small free energy barriers necessary for the fast conduction observed experimentally. This implies that ion-protein association is ultimately controlled by a delicate balance of very strong interactions. Frequently, permeation involves th
e partial dehydration of an ion, followed by the binding to a proteinaceous environment. This archetype is well illustrated by the crystal structure of the KcsA channel. The pore of the KcsA channel comprises a wide aqueous vestibular entryway, lined by non-polar residues on the intracellular side, leading up on the extracellular side to a narrow region lined by backbone carbonyl oxygens. This region of the pore, formed by the residues corresponding to the signature sequence TTVGYG common to all K+ channels, acts as a "selectivity filter" by allowing only the passage of nearly dehydrated K+ ions across the cell membrane. In such narrow molecular pores, a permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with the backbone carbonyl oxygens.
The most informative strategy to address such issues is to compute the multi-ion PMF corresponding to the microscopic process in question (Berneche and Roux, Nature 2001). In particular, the calculation of the PMF enables us to pin-point the location of the largest barrier opposing the passage of a single Na+ ion while there are two K+ ions elsewhere in the pore. We carry those type of calculations using umbrella sampling MD simulations. Another strategy is free energy perturbation (FEP), which allows to compute the relative free energy of different ions at precise location in the pore.
There are 2 sub-projects:
1) Compute the multi-ion PM for Na+ permeation through the KcsA channel using the open state structure that was recently determined by X-ray crystallography in the Perozo laboratory. We have already done a similar calculation for the KcsA in the closed state (Egwolf and Roux, JMB 2010). Umbrella sampling MD simulations are used to obtain W(z1,z2,z3) the 3-ion PMF function of the coordinate of the 3 ions in the selectivity filter. To understand the effect of selectivity, two systems must be considered: with 3 K+ ions, and with 1 Na+ and 2 K+ ions. Based on our experience with similar computations, we know that a grand total of 3931 MD window simulations is needed for two systems. Each window should be simulated for 0.6 ns, the first 0.1 ns being used for equilibration and the last 0.5 ns for sampling proper, for total aggregate MD simulation time of 2.4 microseconds for each of the two systems. The unbiased 3D PMFs are then calculated using the weighted histogram method (
WHAM). The simulations are generated with NAMD, which is the most efficient program for classical MD.
2) Use FEP to compute the relative free energy of Na+ and K+ in a KcsA pore with DFT/MM simulations. For this computation we are using CHARMM combined with the DFT program DEMON (developed by Denys Salahub in Calgary). This enables us to treat the ions and the nearby protein atoms with DFT and the remainder with the force field of molecular dynamics.
Software requirements
NAMD, CHARMM, DEMON
Expected number of project members:
Benoit Roux, David Medovoy (multi-ion PMF calculation) and Chris Rowley (selectivity with density function theory and MD force field)
REFERENCES
Noskov, SY; Berneche, S; Roux, B
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. NATURE Volume: 431 Issue: 7010 Pages: 830-834 Published: OCT 14 2004
Egwolf, B; Roux, B
Ion Selectivity of the KcsA Channel: A Perspective from Multi-Ion Free Energy Landscapes. JOURNAL OF MOLECULAR BIOLOGY Volume: 401 Issue: 5 Pages: 831-842 Published: 2010
Current: undetermined amount
Justification: The umbrella sampling calculations described here constitute a major part of the PhD thesis of David Medovoy, a graduate student in Biophysics at the University of Chicago. The total requested allocation for this project is: 500,000 SU = (3931 windows) * (0.6 ns/window) * ((8*cores)*(12 hour)/ns).
The planned FEP simulations for with DFT/MM will be carried out by Chris Rowley, a postdoc in the lab who has a fellowship from the Canadian NSERC. His work will be a new attack on the problem. Never before has someone computed relative free energies in those channels with DFT/MM. We anticipate this those FEP calculations will require about 500,000 SUs during the year. Demon scales up to about 64 processors, but we are investigating the dependencies on grid density (in DFT) to see how it affects the performance.
Requested: 1000000
A specific reason has been given:
For the first time, a new xray structure of a sodium selective channel just appeared. We knew this was coming. We urgently need some SUs to start this competitive project right away.
This needs to be approved and the final allocation amount decided upon.
Thank You,
The LCRC Accounts System
