Excitation of torsional modes of proteins via collisional energy transfer: A quantum dynamical approach

Quantum dynamical calculations have been carried out on the excitation of the torsional vibrations of a protein by collision with a solvent molecule. This energy transfer process represents the first step in the unfolding of the protein. The method developed for this purpose is the torsional close coupling, infinite order sudden approximation. Both time-independent and time dependent methods are used to solve the scattering problem and individual excitation of all the torsional modes of the protein is treated. The method is applied to the excitation of the HIV protein gp41 colliding with a water molecule. This protein has 1101 atoms, 56 amino acids, and 452 torsional modes. A major mode-selective effect is found in the computations: it is much easier to excite backbone torsions than sidechain torsions in the protein. In addition, resonances arise in the collisional process and these complexes involve temporary trapping of the water molecule inside the pockets of the protein. (C) 2002 American Institute of Physics.