Biology Reference
In-Depth Information
such as cars, molecular machines must be driven by free energy derived from
chemical reactions, but the mechanism by which these processes manage to drive
molecular machines is not yet fully understood. One possibility is suggested by the
conformon theory
, according to which all molecular machines are driven by
chemical reaction-derived or ligand binding/de-binding-induced
mechanical
strains
stored in sequence-specific sites in biopolymers known as the
conformons
(see Sects.
8.2
and
11.4.1
for the mechanisms of conformon generation).
11.4.1 The Conformon Model of “Biomotrons”
There are several related terms used in the fields of molecular biology and the
emerging field of single-molecule enzymology (Xie 2001; Deniz et al. 2008) such
as “molecular energy machines” (McClare 1971, 1974; Welch and Kell 1986),
“molecular machines,” “molecular motors” (Astumian 2000, 2001), “molecular
rotors,” “molecular switches,” “Brownian ratchets,” “molecular catalysts,” and
“protein machines” (Kurzynski 2006). We can regard all these terms as representing
different
species
(or
tokens
) of the same
class
(or
type
) of objects which may
conveniently be referred to as “biomotrons,” a term coined by one of the pioneers
of the single-molecule mechanics, T. Yanagida (
http://www.wtec.org/loyola/word/
mo
tor
s.” The main purpose of this section is to present the following two assertions:
1. All
biomotrons
are driven by
conformons
.
2. Conformons are generated in
biomotrons
from exergonic chemical reactions or
exergonic ligand-binding and de-binding processes, based on the generalized
Conformons are the mechanical energies stored in biopolymers in the form of
conformational strains (Chap.
8
and Sect.
11.3.2
). Since work or energy is defined
as (
energy
)
(
force
)(
displacement)
, force is the rate of change of energy with
respect to displacement. In other words,
energy
and
force
are intimately related so
that one can be used to derive the other, given the numerical value of the displace-
ment and the associated potential energy function. It is for this reason that
conformons can be used to produce molecular forces inside biopolymers.
In
addition, conformons can be generated from chemical reactions through the
generalized Franck-Condon mechanisms as shown in Fig.
8.1
, thus making
conformons
as the realistic molecular mechanisms for transducing
chemical energy
to
mechanical energy
in muscle contraction and other molecular motions or
movements (Astumian 2000, 2001).
The conformon mechanism was first applied to muscle contraction in Ji (1974b),
Fig. 6 on p. 223, reproduced in Fig.
11.34
). The essential content of this mechanism
is depicted in Fig.
11.31b
in terms of symbols rather than pictures. In Fig. 6 of Ji
(1974b) and Fig.
11.34
,
conformons
are represented as a stretched spring attached to
the myosin head (also called subfragment-1 of myosin, or S-1).
¼
