Our work on molecular motors focuses on understanding the mechanisms used by these molecules to convert free energy, stored in the forms of chemical bonds or ion gradients, into mechanical work. Most recenlty, our work has focused on dynein. Homology modeling is being used to generate an accurate structure of this molecule that will then be used in coarse-grained molecular dynamics simulations to understand the conformational changes that are used to generate forces.
We are also interested in developing numerical methods for studying force generation by molecular motors. Recently we have extended our methods to include the biophysical properties of the linkage that connects the motor to its cargo.
Coupling of Structural and Kinetic Models of Molecular Motor Dynein
Using a coarse-grained structural model for two-headed dynein and a hybrid of molecular dynamics and Monte Carlo simulations, we explore the mechanical properties of dynein stepping, including: a structurally biased search for binding sites, step-size distribution, mechanical modulation of transition rates, and the dependence of these features on the orientation and flexibility of the motor’s interaction with the microtubule. By simulating the processive motion of dynein, we demonstrate the consistency of our structural model and earlier kinetic studies with experimental observations.
Serohijos AWR, Tsygankov D, Liu S, Elston TC, Dokholyan NV. Multiscale approaches for studying energy transduction in dynein. Phys Chem Chem Phys. 2009 Jun 28; 11(24): 4840-50.
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Energy transduction in dynein
Intracellular active transport is driven by ATP-hydrolyzing motor proteins that move along cytoskeletal filaments. In particular, the microtubule-associated dynein motor is involved in the transport of organelles and vesicles, the maintenance of the Golgi, and mitosis. However, unlike kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery, due primarily to the lack of a high-resolution molecular structure. Using homology modeling and normal mode analysis, we propose a complete atomic structure and a mechanism for force generation by the motor protein dynein.
The role of motor-cargo linkage in molecular motors
The development of single-molecule techniques for measuring the biophysical properties of molecular motors has motivated the use of mathematical models to elucidate the mechanisms used by these proteins for force generation. Processive motors, such as kinesin, myosin, and dynein, are used for transporting vesicles within cells and for force generation during processes such as mitosis. In general, processive molecular motors consist of two head domains and move along microtubule or actin polymers. The heads interact with specific binding sites along the polymer track and are connected through a stalk that extends from the neck region of each head. The stalk ends in a tail domain that is used to connect the motor to its cargo or to adjacent polymers. Until recently most of the models of molecular motor function did not take into account the biophysical properties of the stalk region that connects the motor to its cargo. However, it is becoming increasingly clear that this linkage can have important consequences on the performance of the motor.