Biology Reference
In-Depth Information
where the bold letters are vectors having both a magnitude and a direction and
regular letters indicate scalar quantities. Also, energy is equivalent to the work
performed by a mass when it is moved by force
F
along distance
L
:
¼
¼ FL ¼ð
Force
Þð
Displacement
Þ
Energy
Work
(8.6)
Therefore, Eq.
8.6
guarantees that, given the requisite molecular mechanisms
(i.e., the generalized Franck-Condon mechanism; see below), conformons can
generate goal-directed molecular forces within biopolymers.
Proteins are unique among biopolymers in that they are the only
macromolecules (except for some RNA molecules acting as ribozymes; see
through catalysis. That is, enzymes are the only molecules that can convert
chemical energy
into
mechanical energy
by generating molecular forces inside
them. The precise molecular mechanisms by which proteins catalyze the chemi-
cal-to-mechanical energy conversion are not yet fully understood, despite inten-
sive investigations over the past half a century. There are many competing
theories to account for the so-called
force-generating mechanisms
in molecular
motors and machines. These include the
molecular energy machine
theory
(McClare 1971),
Brownian ratchet
hypothesis (Astumian 2000, 2001), and a
nonequilibrium statistical thermodynamic model
(Qian 2006, 2007). The
conformon theory of molecular machines first proposed in (Green and Ji 1972a,
b) and further developed and elaborated on the basis of the generalized
Franck-Condon principle (GFCP) (Ji 1974a, b, 1985a, b, 1991, 2000) is unique
among these because (1) it is the only theory providing a principled (i.e., based on
GFCP) molecular and submolecular mechanism to couple chemical reactions to
force generation within proteins (Ji 1974a, b, 2000, 2004a) and (2) it is consistent
with and can accommodate all the other competing theories and hypotheses on the
mechanisms of action of molecular machines and motors.
It is now generally accepted that molecular machines play fundamental roles in
carrying out molecular processes inside the cell (Fig.
8.1
)(Alberts1998;Bakerand
Bell 1998). Most recent evidence indicate that at least some motions of molecular
machines are driven by conformational strains of biopolymers (see “DNA scrunching”
or “DNA-scrunching stress” in Kapanidis et al. (2006); Revyakin et al. (2006).
However, the general mechanisms by which these molecular machines are powered
and driven by exergonic (i.e., free energy-releasing) chemical reactions are not yet
clear. One realistic possibility is provided by the
conformon theory of molecular
machines
proposed over three decades ago (Green and Ji 1972a, b; Ji 1974b,
1991, 2000) (this chapter). The term “conformon” was coined by combining two
stems, “conform-” indicating “conformations” of biopolymers and “-on” meaning
a mobile, discrete material entity. Conformons are defined as follows (Green and Ji
1972a, b; Ji 1974a, 1979, 1985a, b, 1991, 2000, 2004a):
Conformons are sequence-specific conformational strains of biopolymers that carry
mechanical energy and genetic information necessary and sufficient to effectuate any
goal-oriented movement of biopolymers inside the cell.
(8.7)
