Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595

Article Abstract:

The effective fragment potential quantum mechanical-molecular mechanical (QM/MM) method is applied to optimize geometry configurations of a large fraction of the kindling fluorescent protein asFP595 around the chromophore region. Results support the assumption that the dark state of asFP595 corresponds to the anionic or zwitterionic trans-conformation, while the kindled state corresponds to the anionic cis-conformation.

Conformational analysis

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Accurate free energies of micelle formation

Article Abstract:

The free energy of micelle formation for model surfactants in a Lennard-Jones solvent by employing a hybrid semi-grand Monte Carlo simulation scheme in combination with umbrella sampling and configurational bias techniques is determined. The results open up the way for the calculation of critical micelle concentrations using realistic atomic force fields.

Micelles, Gibbs' free energy, Monte Carlo method, Monte Carlo methods

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Protonation of the chromophore in the photoactive yellow protein

Article Abstract:

The phenomena involved in the protonation reaction in the photoactive yellow protein (PYP) and the requirements for proton transfer are studied. The analysis has shown that direct environment of the proton is very vital for this reaction.

Photoreceptors, Mechanical properties, Structure

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