Biology Reference
In-Depth Information
Energy
Reduced
Oxidized
Configurations
Conformations
Evolutionarily
Conserved Residue
Networks
(
Conformons
)
(
Conformers
)
(
Molecules
)
Fig. 11.21 A diagrammatic representation of the relations among
configurations
and
conformations
on the one hand and between
conformers
and
conformons
on the other. Multiple
conformational energy levels are also available for the reduced configuration of a molecule but are
not shown for brevity. The energy scale is approximate
freedom (or the
bioinformation or bioinformatic
dimension) is thought to be
manifested in the form of evolutionarily conserved amino acid residues as indicated
on the right-hand side of Fig.
11.21
. That there indeed exists such an internal degree
of freedom in enzymes was strongly suggested by the finding that many families
of enzymes, receptors, and DNA-binding proteins are characterized by unique
networks of a small number (10-25% of the total) of amino acid residues that are
evolutionarily conserved and coevolved (Lockless and Ranganathan 1999; S
€
uel
et al. 2003; Poole and Ranganathan 2006).
Another distinguishing feature between these two classes of molecules is that
micromolecules are too small to harbor any long-lived internal conformational strains
or kinks, whereas biomacromolecules are large and complex enough to retain
relatively stable internal
conformational strains
produced either during their
syntheses on the ribosomes (Klonowski and Klonowska 1982) or during their cata-
lytic cycles. Such conformational strains have been variously referred to as
conformons
(Green and Ji 1972a, b; Ji 1974b, 2000, 2004a),
frustrations
(Anderson
1983, 1987),
mobile defects
(Lumry 1974; Lumry and Gregory 1986), or
SIDDs
(Stress-Induced Duplex Destabilizations; Benham 1992, 1996a, b). It is here
suggested that the concept of the conformational
gates
that are postulated to control
the rates of enzymatic reactions in the
stochastic model of enzymic catalysis
proposed
by Kurzynski (1997, 2006) can also be viewed as equivalent to
conformons
,sinceno
gate
can be opened or closed at right times for right durations without utilizing
mechanical energy
and
control information
both stored in local conformational
strains in proteins. There are other interesting commonalities between the
conformon
theory of molecular machines
(Ji 1974a, b, 2000, 2004a) and
the stochastic model of
protein machines
proposed by Kurzynski (1993, 1997, 2006).
