The Conformon - Molecular Theory of the Living Cell - page 242

it can be applied to both a machine (viewed as a network of the components of a
machine) as well as to the network of molecular machines themselves. Thus, we
may formulate what may be referred to more generally as the “Dual Control
Hypothesis of Molecular Machines” (DCHMM) as follows:
The direction of movement of molecular machines (or their components) is determined by
thermodynamics through free energy changes and their speed or timing by kinetics
implemented by conformons. (8.20)
Statement 8.20 may be represented using the concept of vectors. There are three
key elements in Statement 8.20 - (1) molecular machines, (2) the direction of
motion of the machines, and (3) the speed or timing of machine motions. We may
compare (1) with the coordinates of the origins of vectors, (2) with the angle of the
vectors, and (3) with the lengths of vectors.

8.6 Ion Pumps as Coincidence Detectors

Since enzymes can be viewed as coincidence detectors (see Sect. 7.2.2 ) and since
the Ca ++ ATPase is an enzyme, it is natural to view the ATP-driven active transport
of Ca ++ ion, shown in Fig. 8.6 , as an example of an enzyme-catalyzed coincidence-
detecting event as explained in Fig. 8.8 .
Here, we identify the chemical processes of ATP hydrolysis within the C domain
and the physical processes of Ca ++ ion movement across the membrane through the
T domain as the two events that are synchronized or correlated by the ion pump,
and the set of all the space- and time-ordered motions of the molecular entities
necessary to couple the C domain and T domain is treated as the coincident events
or long-range molecular correlations (to use the terminology of the physics of
critical phenomena [Domb 1996]). The calcium ion pump, being a coincidence
detector , is postulated to execute an orderly movement of catalytic amino acid
residues located in the C and T domains in such a manner as to hydrolyze ATP if
and only if Ca ++ ions move through the requisite binding sites in the T domain in
the right direction, namely, from the cytoplasmic to the luminal side when the ATP

Brownian Motions
(Random motions
of Ca ++ and ATP) Ordered

Motions C alcium Ion

Pump

(e.g., Active

Chemical Reactions transport

of Ca ++ )

(ATP electronic

transitions)

Fig. 8.8 Conformon-driven calcium ion pumping viewed as a coincidence-detecting event
catalyzed by the Ca ++ ATPase. This figure represent the application of the general enzymic
mechanisms, Fig. 7.6 , to the case of the calcium ion pump. See text for details