Computational simulations of supermolecular complexes

Computational simulation techniques, targeted molecular dynamics (TMD) and the quantized elastic deformational model (QEDM, a modified normal mode analysis) in particular, have been employed to determine functionally relevant motions (motions required to perform a specific biological process) of six supermolecular complexes (SMC's): F1F0-ATP synthase, lactose repressor protein, HIV-1 reverse transcriptase, AAA p97, lipid bilayer, and bacterial flagellum. These SMC's are involved in a diverse number of biological processes - production of energy, genetic and allosteric regulation, propagation of viral infection, and cell structure integrity. Understanding the motions of SMC's, as opposed to individual proteins or molecules, is a fundamental step towards determining detailed functional mechanisms. (1) TMD trajectories of F1-ATPase are used to resolve the motions and interactions that occur during the 120° rotation step of the gamma subunit. An ionic track of arginine and lysine residues on the protruding portion of the gamma subunit plays a role in guiding the motions of the beta subunits. (2) The allosteric transition of lactose repressor protein from the repressed (DNA-bound) to the induced (IPTG-bound) state is simulated using TMD. Non-covalent interactions of three interconnected pathways are described. Pathway 2 involves reorganization at the dimer interface and formation of an H74-H74' pi-stacking intermediate. (3) TMD is utilized to investigate the translocation mechanism of HIV-1 reverse transcriptase. The atomic-level interactions between electrostatic (i.e., K263) and hydrophobic (i.e., W266) residues and the DNA primer strand are highlighted. (4) The proposed negative-cooperative ratchet-mechanism between the D1 and D2 rings of p97 is illustrated by means of a QEDM analysis. (5) The intrinsic fluctuations of a DPPC lipid bilayer are investigated via QEDM and elucidate a low-frequency sound mode. (6) QEDM is used to calculate the dimensionless twist-to-bend ratio (EI/GJ) of bacterial flagellar hook and filament. Both ratios are less than one, indicating that within each structure bending is favored over twisting. A theoretical Young's modulus for the hook is proposed, which is orders of magnitude smaller than experimentally determined Young's moduli of the filament. The research results in this thesis are also placed in context of existing experimental data, and in some cases propose future experimental work