Structure, function, and dynamics of cell motility proteins

Molecular dynamics (MD) simulation techniques have been employed to investigate structure and function relationships in cell motility proteins at atomic resolution. (1) To analyze motions in cell motility proteins an algorithm is described to identify and visualize the movements of rigid domains about common hinges in proteins. In comparing two structures, the method partitions a protein into domains of preserved geometry and characterizes the relative movement of domains by effective rotation axes. (2) Simulated in solution, the calcium-binding protein calmodulin exhibits large conformational changes on the nanosecond time scale. The central a-helix, which has been shown to unwind locally upon binding of calmodulin to target proteins, bends and unwinds near residue Arg74. The major structural change is a reorientation of the two Ca2+-binding domains with respect to each other and a rearrangement of α-helices in the N-terminus domain which make the hydrophobic target peptide binding site more accessible. This structural rearrangement brings the domains to a more favorable position for target binding, poised to achieve the orientation observed in the complex of calmodulin with myosin-light-chain-kinase. (3) In MD simulation, water molecules diffuse into the buried nucleotide binding site of the cytoskeletal ATPase actin along two distinct pathways. Of particular interest is the "back door" diffusion pathway which is believed to be relevant for the dissociation of phosphate (Pi) after ATP hydrolysis. Adhesion forces were measured as Pi was forced to unbind through the back door dissociation pathway. Protonation of Pi is required for unbinding from the ADP-associated Ca2+ -ion. Actin's methylated His73 is a putative modifier of Pi release. The simulations suggest that His73+ stabilizes unprotonated Pi, thereby inhibiting dissociation from actin. (4) Conformational changes in the microtubule-based kinesin motor which can be attributed to the force-producing ATP hydrolysis are predicted. The results indicate an allosteric coupling between the nucleotide pocket and the microtubule binding site of kinesin. The activation of two conformational switches at Gly234 and Ser202 triggers a cascade of structural changes in the motor domain. Our results suggest that the nucleotide is an allosteric modifier of kinesin's microtubule-binding state: In the presence of ATP, kinesin's putative microtubule binding regions form a strong-binding interface to the microtubule. In the presence of ADP, the interface becomes more convex, resulting in a loss of contact with the microtubule.U of I Onlythesi