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(Ji 1974a, b) already embodies these features of coincidence detectors which were
recognized only recently. The concept of coincidence detectors are widely used to
account for neuronal behaviors (Mikula and Niebur 2003).
4.2 Molecular Machines, Motors, and Rotors
The living cell can be viewed as space- and time-ordered systems (or networks) of
molecular machines
(Alberts 1998), proteins that can utilize the free energy of
chemical reactions such as ATP hydrolysis to carry out goal-directed or teleonomic
molecular motions (Ishii and Yanagida 2000). The molecular mechanisms respon-
sible for such goal-directed molecular motions of biopolymers are postulated to be
provided by
coformons
, conformational strains resident in sequence-specific sites
within biopolymers that are generated from chemical reactions based on the
generalized Franck-Condon principle (Sect.
8.2
) (Green and Ji 1972a, b; Ji
1974a, 1979, 2000, 2004a).
Concept of molecular machines (McClare 1971; Ji 1991; Alberts 1998; Ishii and
Yanagida 2000, 2007; Xie and Lu 1999; Xie 2001) is one of the most important
contributions that biology has made to our understanding of how the living cell
works. Like macroscopic machines, molecular machines must exert forces on their
environment during their work cycle and this means that molecular machines must
possess mechanical energies stored in them, since energy is required to generate
forces. Such stored internal energies of molecular machines have been referred to as
conformons
(Green and Ji 1972a, b; Ji 1974a, b, 1991, 2000). Molecular machines
that perform work on their environment without utilizing internally stored mechan-
ical energy (e.g., conformons) violate the First and Second Laws of Thermodynam-
ics (McClare 1971).
Most metabolic processes inside the cell are catalyzed by combinations of two or
more proteins that form functional units through noncovalent interactions. Such
protein complexes have been variously referred to as metabolons (Srere 1987),
modules (Hartwell et al. 1999), hyperstructures (Norris et al. 1999, 2007a, b). The
number of component proteins in complexes varies from 2 to over 50 (Aloy and
Russell 2004). More recent examples of the protein complexes that involve more
than 50 components include eukaryotic RNA polymerases, or
transcriptosomes
(Halle and Meisterernst 1996),
spliceosomes
(catalyzing the removal of introns
from pre-mRNA),
molecular chaperones
(catalyzing protein folding), and
nuclear
pore complexes
(Blobel 2007; Dellaire 2007; Dundr and Misteli 2001). These
protein complexes are theoretically related to dissipative structures of Prigogine
be convenient to view them as members of the same class of molecular machines
called “dissipatons” defined in Sect.
3.1.5
.
