Protein Motion
The lectures will be structured according to the following
topics: Fundamental Interactions in Structural Biology and Fundamentals of
Protein Architecture; How Proteins Move: Molecular Dynamics; How Proteins Move:
Normal Mode Dynamics; Mesoscale Modeling of Nanomachines. An expanded version
follows. Over the last three decades computer simulation have been able to bring
atomic motion to structural biology. Such motion is not seen in experimental
structural studies but is relatively easily studied by applying law of motions
to models of the proteins and nucleic acids. By bringing molecular to life in
this way, simulation complements experimental work making it much easily to
understand how proteins biological macromolecules function. After introducing
molecular structure and the fundamental force that stabilize it, we consider the
two complementary approaches to molecular motion. In the final lecture, we
explore models and methods suitable for studying the structure and dynamics of
very large protein complexes that we term "nanomachines". We using a novel
approach to molecular morphing to study the large conformational changes
associated with the power stroke of the muscle motor, myosin. We compare the
normal modes of the myosin head piece at different levels of atomic detail. The
models vary by an order of magnitude in the number of interaction centers and
two orders of magnitude in the number of degrees of freedom. These same methods
are applied to a variety of other large complexes that play central roles in the
molecular biology of the cell.