Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories

A systematic method of representing and analyzing the intramolecular strains in proteins is proposed. For illustrative purposes, the method is applied to the N-terminal fragment of the human T-cell glycoprotein CD4. The method is based on the singular value decomposition (SVD) of molecular dynamics (MD) trajectories. The slowest three modes of motion that carry information along the protein molecule over large length scales are analyzed, so as to characterize the collective motions and the resulting strains along the three principal axes of the protein. Strong cooperative motions of different types, mainly wave-like, wagging, wiggling, breathing, bending and shearing motions, and rigid body rotations are distinguished. The mean-square fluctuations of Cα-atoms induced by the three dominant modes are found to exhibit a closer correlation with the experimental temperature factors in the presence of solvent.