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Yanagida 2000, 2007; Deniz et al. 2008). SME differs from the conventional
ensemble-averaged enzymology (EAE) in one important respect: Whereas EAE
studies time-dependent
concentrations
of materials involved in chemical reactions,
SME investigates time-dependent
probabilities
of single-molecule events such as
the activation or deactivation of an enzyme (Fig.
11.17
), stochastic movements of
molecular motors along DNA, actin filament (Fig.
11.33
), or microtubules. It is here
suggested that SMM and SME obey the same set of the principles and rules
(described below) on which what is here called the “single-molecule stochastic
mechanics” (SMSM)
is grounded and hence are synonymous with it:
i.e.,
SMM
¼
SME
¼
SMSM.
There appears to be only a small number of the physical principles and rules that
underlie SMSM:
1. All molecular machines are driven by mechanical energy packets known as
conformons
that are stored in biopolymers as sequence-specific and mobile
conformational deformations (Green and Ji 1972a, b; Ji 1974b, 1991, 2000,
2004a).
2. Conformons can be generated from chemical reactions in three steps (see
Fig. 8.1 in Sect.
8.2
and Fig.
11.30
):
(a) Enzymes borrow thermal energies from their environment to produce
virtual
conformons
(as a result of
thermal fluctuations
) lasting for less than the time,
t
, required for enzymes to complete their machine cycles.
(b) Virtual conformons mediate the catalysis of an exergonic (i.e., free-energy-
supplying) physicochemical processes within their lifetimes.
(c) Enzymes avoid violating the Second Law by “paying back” the thermal
energy borrowed in Step (a) by letting the free energy released from the
physicochemical processes equilibrate with its environment within times less
than
t
and also by synchronously stabilizing the virtual conformons with one
or more products generated from the exergonic chemical reactions (Ji 1979).
3. All molecular machines perform work on their environment (e.g., actin filament
in the case of myosin, ions in the case of ion pumps) through energy transfer
during the coupled phase of
the machine-environment
interaction cycle,
preventing slippage (Ji 1974b).
Items (2)(a) and (2)(b) may appear to violate the traditional formulation of the
Second Law of thermodynamics, according to which no
thermal energy can be
utilized to do work in the absence of temperature gradients
, but this is not the case,
because these mechanisms obey the “molecularized” Second Law of thermody-
namics (MSLT) formulated by McClare (1971) (see Statement 2.5 in Sect.
2.1.4
).
Rule (2)(b) appears reasonable in view of the fact that
virtual conformons
can last
for times much longer than the time required for electronic transitions (or covalent
bond rearrangements) and hence the generalized Franck-Condon principle (GFCP)
can be applied to them (Sect.
2.2.3
). Single-molecule measurements indicate
that conformational changes attending enzymic actions are slower than the
