Molecular dynamics studies of proteins under perturbations

The responses of proteins to different perturbations are simulated by molecular dynamics simulations, analyzed by theoretical models and compared with observations. (1) The response of temperature to temperature quenches and velocity reassignments are described in terms of the temperature autocorrelation function by the harmonic approximation. Models were developed to show that the decay of the response, an echo, arises from anharmonic interactions which dephase periodic motions. (2) We demonstrate that the dipole moment of a protein responds to a constant electric field applied for picoseconds or less through dipolar relaxation as well as through an echo. This phenomenon can be explained through a model in terms of Langevin oscillators and related to observations in sub-picosecond spectroscopy. (3) The coupling between the electronic states of retinal and the protein matrix in the early picosecond events of the bacteriorhodopsin (bR) photocycle is characterized by the energy difference $\Delta E(t)$ between the excited state and the ground state. Our simulations indicate that the rise time of the J intermediate, i.e., about 500 fs, corresponds to a polarization of bR due to the photoexcitation. Our simulations also support the suggestion that the J $\rightarrow$ K transition is due to vibrational cooling of a retinal heated through photoisomerization. (4) Simulated annealing is used to carry out the study of the M intermediate in the bR photocycle. Our simulations indicate that the M intermediate consists of a sequence of states connected with protein conformational change and reconfiguration of waters, particularly a 60$\sp\circ$ bend of helix F at the cytoplasmic side, and the changes in the connection between water and the Schiff base. (5) The primary electron transfer in the photosynthetic reaction center of Rhodopseudomonas viridis is studied by applying the spin-boson model to describe the coupling between protein motion and electron transfer. We present the temperature and redox energy dependence of the electron transfer rates which are found in agreement with observations and also with Marcus theory at high temperatures.U of I OnlyETDs are only available to UIUC Users without author permissio