The conformational analysis of adenosine triphosphate by classical potential energy calculations

Abstract

AbstractThe conformational analysis of adenosine triphosphate was conducted by using classical potential energy calculations. All rotatable bonds were examined, i.e., no dihedral angles were fixed at predetermined conformations except for the ribofuranose ring, which was held in the C(3′)‐endo conformation—the conformation observed for adenosine in the crystal state.The energy terms included in the total energy expression consist of nonbonded pairwise interaction, electrostatic pairwise interaction, free energy of solvation, and torsional bond potentials.Two separate approaches were used in the conformational analyses. The first consisted of a sequential fragment approach were four bonds were rotated simultaneously at 30° increments. Each fragment overlapped the preceding one by at least one bond. All rotors were then simultaneously examined at their minima and at ±15°. The second approach consisted of a coarse grid search where all rotors were examined simultaneously, but only at staggered positions. The low‐energy conformations thus obtained were then used as starting conformations for a minimization routine based on the method of conjugate directions. The first approach required about 40 hr of central processing unit (CPU) computer time, while the coarse grid/minimization approach required about 4 hr of CPU time.Both the sequential fragment approach and the minimization approach yielded lowest‐energy conformations which are remarkably similar to the solid‐state conformation of C(3′)‐endo ATP.