Tryptophan structure and dynamics using GROMOS

The desire to use tryptophan as a fluorescent probe to study protein motion has motivated studies on tryptophan in aqueous solution. Tryptophan's biexponential fluorescence decay in solution has given rise to models which account for this behavior by postulating the existence of rotamers about the C/sub α/-C/sub β/ bond. These models require that the rotamers do not interconvert during the fluorescence lifetime; this assumption has not been verified. Further, there are certain peculiarities in assigning particular fluorescence lifetimes to these rotamers on the basis of proximity of the charged quenching groups. To address these issues the authors have used energy minimization and classical molecular dynamics as bases for transition rate and population estimates. These suggest that the C/sub β/-C/sub γ/ dihedral (chi/sub 2/) determines the fluorescence lifetime for equilibrating groups of C/sub α/-C/sub β/ rotamers. The energy minimization was similar to that already reported in the literature, but with GROMOS charges (for tryptophan in solution) and GROMOS interaction potentials. A potential surface for the energies of chi/sub 1/,chi/sub 2/ conformations was generated by constraining the dihedrals and minimizing the potential energy of the remaining degrees of freedom. Energy barriers between conformers range from about 3 kcal/mol to about 8 kcal/mol. The smaller barriers correspond to chi/sub 1/ rotations. Seven 100-psec classical dynamics trajectories were calculated for the system coupled to a heat bath with a time constant of 0.1 psec (solvent molecules are not explicityly included)