Mei Shi Advisor-Dr. Balbuena University of South Carolina REU-Summer of 2002

Introduction Ion channels are important not only for biological functions such as electrical signal conductance, but also for applications in fuel cells and batteries. The design of the ion channel is modeled after KcsA potassium ion channel from the bacteria known as Streptomyces lividans. Molecular Dynamic Simulations involves the calculation of molecular motions with respect to time based on a set of initial conditions. Computational software called DL_POLY2 is used. Input files like CONFIG, FIELD and CONTROL are necessary to run the simulation..

Background Information

4 identical protein subunits Each subunit is consisted of 3 helical segments : outer helix, inner helix, and pore helix.

Schematic picture of the KcsA Potassium Ion channel

 4 carbonyl oxygen atoms are exposed to the extracellular environment.  Displace half of the ion’s hydration shell  The carbonyl oxygen atoms in the filter acts a surrogate water oxygen that form the hydration shell.  The selectivity filter is formed by a amino acid sequence known as the K + channel’s signature sequence

 K + channel must mediate the transfer of a K + ion from its hydrated state in solution to its dehydrated state in the selectivity filter.  K + channel must favorably select K + ion over Na + (factor of to 1). Potassium ion Charge---+1 Radius Å Sodium ion Charge---+1 Radius Å

Theory of selectivity Ion in solution is surrounded by waters of hydration. The smaller the ion, the more highly localized its charge and stronger the electric field, which makes smaller Na + exert a stronger attraction on the water surrounding and obtain a smaller size of hydration shell than the bigger K + does.

The diameter of the selectivity filter is just enough allowing the dehydrated K + ion through, but is too wide for the Na + ion to bind and enter the filter and too narrow for the hydrated Na + ion to pass through. The selectivity of the potassium ion channel for K + over Na + can be investigated by adjusting the diameter of the selectivity filter and the positions of the charged pseudoatoms lining the filter.

A General Representation of the Cellular Environment Cellular membrane---layers of neutral pseudoatoms that have the characteristics of methane molecule such as their weight (16.00 au) and their Van der Waal sradius (1.95 Å) Ion channel---a cylindrical pore that is embedded in the membrane layer. The selective region of the pore is lined with charged pseudoatoms that exhibit characteristics of carbonyl oxygen atom on a peptide backbone such as their charge (-0.38). SPC model of water molecules are placed on both sides of the membrane as well as inside the channel along with different types of ions such as chlorine ion, sodium ion and potassium ion.

Square anti-prism

Top viewSide view water Na+ Membrane Filter atomsK+ Cl-

500 steps apart or 0.5 ps apart

500 steps apart Or 0.5 ps apart

A better side view

Result and discussion The diameter of the filter arranged from 4.7 Å to 7.9 Å, and so far the result have yet to show selectivity. Ion passage through the channel seems to depend only on their initial positions and their charge. Single file motion for water as well as ions was exhibited in passing through the channel.