The sequences of several members of the myosin
family of molecular motors are evaluated using ASP (Ambivalent
Structure Predictor), a new computational
method. ASP predicts structurally ambivalent sequence elements
by analyzing the output from a secondary structure prediction
algorithm. These ambivalent sequence elements form secondary
structures that are hypothesized to function as switches
by undergoing conformational rearrangement. For chicken
skeletal muscle myosin, 13 discrete structurally ambivalent
sequence elements are identified. All 13 are located in
the heavy chain motor domain. When these sequence elements
are mapped into the myosin tertiary structure, they form
two compact regions that connect the actin binding site
to the adenosine 5′-triphosphate (ATP) site, and
the ATP site to the fulcrum site for the force-producing
bending of the motor domain. These regions, predicted by
the new algorithm to undergo conformational rearrangements,
include the published known and putative switches of the
myosin motor domain, and they form plausible allosteric
connections between the three main functional sites of
myosin. The sequences of several other members of the myosin
I and II families are also analyzed.