Theoretical Study For The Time-resolved Ultrafast Fluorescence Spectra Of Myoglobin

Experiment and simulation is an important method to study the dynamic behavior of biological macromolecules such as proteins. In these experimental studies, a variety of spectroscopy and spectroscopic methods have provided a wealth of information for the study of biological macromolecules. However, due to the experimental methods cannot be directly observed atomic positions and other information, but just respond to the external stimuli, researches can only speculate microscopic dynamical behavior of molecules by measuring the macromolecules. The molecular simulation can track the location and speed of the atoms directly from the microscopic level by solving the Newton equation and the Schrodinger equation, which can provide the most direct observation. However, due to the limitation of the computer processing power and algorithms, the molecular simulation can not deal well with the situation of the large spatial scales and the long time scales in the biological problems. One the other hand, the reliability of the theoretical research is limited by the accuracy of the potential function used. Therefor, the scientists expect to get more rich and more reliable data through the complementary experiment and simulation methods. And with the development of the time-resolved fluorescence technology, study for the ultrafast dynamics of the biological macromolecules may can benefit from it. However, there is a significant discrepancy existing between the experiment and theory in predicted the initial relaxation. The predicted initial relaxation from computer simulation is one-order faster than the ultrafast fluorescence spectroscopy experiment. And the chemical biologists want to know the source of the differences. For the molecular simulations, lack of the explicit polarization effect has been know as the dominant limitation of some contemporary force fields and the limitation may weaken the electrostatic interactions between the molecules and make the molecules move faster.In this work, we want to tell the effect of the electrostatic interactions in the molecular simulations, and investigate the possibility that employing polarization effect can fill the gap between the experiment and simulation. In the simulation, we studied the hydration dynamics of myoglobin with both AMER99SB force field and the polarized protein-specific charges (PPC) in the framework of linear response. And for the PPC, there are three versions of it were fitted and employed in the simulation, which differed in the implementation of solvation effect while fitting the charges. We denoted them as PPC, PPC, PPC". In linear response theory, the characteristic time scales for time-dependent Stokes shift are extracted from the time correlation function C(t) of energy gap between the excited state and the ground state. The results show that although adding the polarization effect to the protein and the solvent can hinder the rotational and translational motion of water molecules and the relaxation of the tryptophan residue in protein, its impact is very limited. In a word, the polarization effect still cannot fill the gap of between experiment and theory, at least under linear response approximation.