We have finished the formulation of a formalism that can be used to elucidate the mechanisms of movement of kinesin motors on microtubules driven by the hydrolysis of ATP based on the mechanical data measured in an in vitro motility assay. In this assay, a sub-micron plastic bead is elastically attached to a single two-headed kinesin motor and the movement of the bead along a microtubule, caused by the interaction of the kinesin and the microtubule, is measured as a function of the ATP concentration in solution and the external force applied to the bead. The formalism should be useful in differentiating the various molecular models proposed for kinesin motors (work by Chen, Yan, and Rubin). We have also finished working on modeling the kinetics of binding myosin sub-fragment 1 to regulated actin in the presence and absence of calcium based on the two-state Hill model ( Hill, Eisenberg, and Green, 1980. PNAS 77: 3186-90) and the three-state Geeves model (McKillop and Geeves, 1993, Biophys. J. 65:693-701). The purpose of this study is to examine whether the Hill model can account for kinetic binding data, specifically for the lag found in the kinetic binding curves when excess S1 binds to regulated actin filaments in the absence of calcium. It had been claimed before that the two-state Hill model is unable to account for such a lag. Thus, an alternative three-state Geeves model was proposed and claimed to be essential for fitting the lag phase. Here we show that the Hill model can account for the lag in the kinetic binding data at least as well as the Geeves model. We further show that both models are indistinguishable in their ability/inability to account for existing kinetic and equilibrium binding data. Thus, the Hill model cannot be ruled out on the basis of existing kinetic and equilibrium binding data (work by Chen, Yan, Chalovich, and Brenner). Another project on which we have made some progress is the molecular dynamics studies of the conformation of kinesin (a microtubule-based molecular motor) bound with different nucleotides. The main purpose is to investigate whether the fluctuations of movement of the residues in the linker region (the region linking the coil-coiled stem to the head or motor part of the kinesin) are different with different bound nucleotides. Due to long computer times needed, the calculations are slow. However, we have found that the fluctuations are large when ADP is bound and small when ATP is bound or without a nucleotide. The results suggest that the dynamics of motion in the linker region may play an important role in the directional movement of kinesin molecules on microtubule (work by Yan and Chen)
