PROTEIN DYNAMICS
How does myoglobin uptake oxygen?
The protein myoglobin has an important biological function: oxygen
storage and transport. However, despite decades of research,
the exact pathway of oxygen diffusion inside the protein
globule towards the iron atom is still unknown.
Does the oxygen molecule travel through myoglobin along a
single dominant pathway before it chemically binds to the iron atom, or is it able to
reach the bull's eye by many different routes? In fact, it is both.
The pathways are revealed through the analysis of the
cavities that are dynamically present in the protein as a result of thermal
fluctuations at normal body temperature. We have
used supercomputers such as VT's SYSTEM-X to perform
molecular dynamics simulations that model these fluctuations; we have
also
developed a set of software tools -- PATHFINDER --
that identify the cavities in the
generated protein structures. This work is to appear in PNAS.