Molecular dynamics simulations of enhanced green fluorescent proteins: effects of F64L, S65T and T203Y mutations on the ground-state proton equilibria.

Molecular dynamics simulations with the Amber force field are carried out to study two mutants of the green fluorescent protein (GFP), namely EGFP (F64L/S65T) and T203Y-EGFP (E(2)GFP). Those variants display an opposite equilibrium between the structural A and B states, associated with neutral and anionic protonation forms of the chromophore. Configurations of those two states are simulated for each variant and the energetics of their equilibrium in the two mutants is studied by evaluating the change in the relative free energy of A and B states (DeltaG(AB)) upon T203Y mutation. The resulting DeltaDeltaG(AB) agrees with the value inferred from absorption measurements. A comparison of the hydrogen bond network around the chromophore rationalizes the different population of state A and B in EGFP and E(2)GFP. On the basis of structural and energetic considerations, a mechanism for destabilization of the neutral chromophore in S65T mutants is proposed. Simulations of the B state of the S65T variant and of WT GFP are also performed for comparison and to test the force field parameters of the chromophore derived for the present calculations. Possible paths of proton transfer leading to nonfluorescent states of the chromophore are discussed in light of the photodynamical behavior of GFP, as revealed by fluorescence correlation spectroscopy and single-molecule experiments.

Coherent dynamics of photoexcited green fluorescent proteins.

The coherent dynamics of vibronic wave packets in the green fluorescent protein is reported. At room temperature the nonstationary dynamics following impulsive photoexcitation displays an oscillating optical transmissivity pattern with components at 67 fs (497 cm(-1)) and 59 fs (593 cm(-1)). Our results are complemented by ab initio calculations of the vibrational spectrum of the chromophore. This analysis shows the interplay between the dynamics of the aminoacidic structure and the electronic excitation in the primary optical events of green fluorescent proteins.

Spontaneous formation and stability of small GaP fullerenes

We report the spontaneous formation of a GaP fullerene cage in ab initio molecular dynamics simulations starting from a bulk fragment. A systematic study of the geometric and electronic properties of neutral and ionized GaP clusters suggests the stability of heterofullerenes formed by a compound with zinc blende bulk structure. We find that GaP fullerenes up to 28 atoms have high symmetry, closed electronic shells, large highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps, and do not dissociate when ionized. We compare our results for GaP with those obtained by other groups for the corresponding BN clusters.