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molecularworkontheactinfilament.Inother words, the conformons present in
cholesterol oxidase are present from the birth of a protein while those generated
from ATP hydrolysis (and other exergonic chemical reactions such as ligand
binding, methylation, oxidation, reduction, etc.) are introduced later in the life
cycle of a protein. For the lack of better terms, we will refer to the former as
static
(or
intrinsic/endogenous
)andthelatteras
dynamic
(or
extrinsic/exogenous
)
conformons. As pointed out in (6) in Sect.
11.3.3
, “static” conformons are closely
related to what is known as the Klonowski-Klonowska conformons (Ji 2000) and
to “frustrations” of Anderson (Ji 2000).
In conclusion, the single-molecule enzymological and mechanical data
measured by two independent groups in 1998 have been rationally accounted for
in terms of the concept of the
conformon
introduced into molecular biology in 1972
(Green and Ji 1972a, b; Ji 1974b, 2000). If the explanations proposed in Sects.
11.3
and
11.4
turn out to be correct upon further investigation, we will be able to
conclude that
it took a quarter of a century for the theoretical concept of the
conformon to be experimentally confirmed with reasonable certainty.
11.4.3 Stochastic Mechanics of Molecular Machines
In Sect.
4.9
, the concept of “info-statistical mechanics” was introduced based
on the
information-energy complementarity
as applied to statistical mechanics.
In the present section, a related term, “stochastic mechanics,” is introduced,
motivated by recent emergence of single-molecule enzymology and mechanics
(Xie and Lu 1999; Xie 2001; Ishii and Yanagida 2007; Deniz et al. 2008). Both
these terms are closely related as forest and trees or as global and local views.
In other words, we may regard “info-statistical mechanics” and “stochastic
mechanics” as global (or forest) and local (or trees) views, respectively, of the
same phenomenon of life on the microscopic level.
We can divide machines into
deterministic
and
stochastic
machines.
Determin-
istic machines
(e.g., computers, cars, washing machines) are macroscopic in size,
robust against thermal fluctuations (i.e., machine component configurations are
not destroyed/rearranged by Brownian motions) and obey deterministic rules.
Stochastic machines
in contrast are microscopic in size (e.g., enzymes, molecular
motors, cells), depend critically on Brownian motions for their functions, and
exhibit stochastic behaviors that can be represented as time-dependent functions
of some random variables (e.g., enzymic activity).
As already mentioned, during the past decade a new field in molecular biology
has emerged variously referred to as “single-molecule mechanics” (SMM) or
“single-molecule enzymology” (SME) (see Sects.
11.3
and
11.4
) as a result of the
development of new experimental techniques such as optical tweezers and Foerster
(or fluorescence) resonance energy transfer (FRET) methods that have enabled
biophysicists to visualize and manipulate single biopolymer molecules (proteins,
DNA, and RNA) and measure their motions in real time, involving forces and
displacements in the ranges of piconewtons and nanometers, respectively (Ishii and
