| THE STRUCTURE WAS MINIMIZED IN 500 STEPS OF POWELL'S CONJUGATE GRADIENT MINIMIZATION | X-PLOR 3.1 WAS USED TO DETERMINE THE MINIMUM ENERGY POSITIONS OF THE POTASSIUM IONS. A VAN DER WALLS RADIUS OF 1.96 A AND A CHARGE OF PLUS ONE WAS USED FOR EACH POTASSIUM ION. A DISTANCE-DEPENDENT DIELECTRIC FUNCTION WAS INCLUDED IN THE NON-BONDED TERMS. THE OPTIONS FOR THE DISTANCE-DEPENDENT DIELECTRIC FUNCTION USED IN THIS PROTOCOL INVOLVE USING A VAN DER WAALS FUNCTION IN COMBINATION WITH A ELECTROSTATIC FUNCTION AND A 1/R-DEPENDENT DIELECTRIC FUNCTION, WHERE R INDICATES THE DISTANCE BETWEEN ATOMS (COULOMB'S LAW). IN ORDER TO SIMULATE AN AQUEOUS ENVIRONMENT, THE DIELECTRIC CONSTANT OF THE SYSTEM WAS SET TO 64. THE SWITCHING FUNCTION FOR THE NON-BONDED INTERACTIONS WAS ACTIVE BETWEEN 7.5 AND 10.0 A. THE NON-BONDED INTERACTION CUT-OFF WAS SET TO BE A SMOOTH TRANSITION BETWEEN 0.5 AND 10.0 A. THE DNA/POTASSIUM COMPLEXES WERE SUBJECTED TO A 500-STEP MINIMIZATION ALLOWING ONLY THE POTASSIUM TO MOVE WHILE THE DNA WAS HELD RIGID. ENERGY MINIMIZATION'S WERE RUN WITH VARIOUS STARTING POSITIONS FOR THE POTASSIUM IONS IN ORDER TO DETERMINE IF THE INITIAL POSITION HAD AN EFFECT ON THE MINIMIZED POSITION. RANDOM STARTING POSITIONS OF THE K+ FROM 5 TO 10 A AWAY FROM THE DNA WERE USED AND THE FINAL RESULTS WERE FOUND TO BE INDEPENDENT OF THE INITIAL COORDINATES OF THE POTASSIUM. THE MINIMIZATIONS WERE CARRIED OUT FIRST WITH ONE POTASSIUM ION PER QUADRUPLEX AND THEN WITH TWO PER QUADRUPLEX. THE POSITION OF THE FIRST BINDING SITE DID NOT CHANGE, UPON ADDITION OF THE SECOND POTASSIUM, FOR EITHER DNA. ADDITIONAL MINIMIZATIONS DID NOT CHANGE THE POSITIONS OF THE POTASSIUM IONS. | X-PLOR |
