Biology Reference
In-Depth Information
According to Fig.
11.23
, a polypeptide with 40 amino acid residues catalyzing
three catalytic processes will have three
conformons
, each comprising 10 amino
acid residues (see the lower left region of Series 5 in Fig.
11.23
). If there is no
overlap among the amino acid residues that constitute two different conformons,
the maximum number of amino acid residues required to generate three conformons
would be 30. If an overlap is allowed, the maximum number would be less than this
number, leading to the prediction that at most 75% of the amino acid residue of the
40-mer polypeptide should be evolutionarily conserved. This prediction seems to be
in agreement with the observation reported by Socolich et al. (2005): Multiple
sequence alignments of the 120 members of the WW domain family revealed that
about 50% (i.e., 17 out of 36) of the amino acid residues of WW domains is
evolutionarily conserved. These conserved residues exhibited the SCA (statistical
coupling analysis) conservation scores greater than 0.5, the background level (see
Fig. 1b in Socolich et al. 2005). The discrepancy between the predicted value of
75% and the observed one of 50% may simply indicate that
An amino acid residue at a given locus on a polypeptide chain can participate in producing
more than one conformons.
(11.21)
Statement 11.21 is reminiscent of the piano keys (
amino acid residues
) which
can be struck (at different times) to produce more than one musical sounds or
melodies (analogous to
conformons
). We may refer to Statement 11.21 as the
conformon composition rule
, which can be more generally stated as follows:
Conformons are generated in a biopolymer from a set of evolutionarily conserved elements
(amino acid residues or nucleotides) that are combinatorially arranged in space and time,
just as musical melodies are generated from the combinatorial arrangements of musical
notes in time.
(11.22)
Just as producing melodies requires a pianist's expending energy by striking a
select set of right keys in a right temporal order, it is clear that generating a
conformon in a conformer of an enzyme by selecting a set of right amino acid
residues arranged in space and time must be paid for by some exergonic processes
such as ligand binding/de-binding and electronic rearrangements (known as
chemical reactions). From the bioenergetics point of view, the production of a
conformon requires coupling two partial processes - one endergonic (free energy-
consuming) and the other exergonic (free energy supplying) (see Fig.
11.30
for
more details).
The fundamental assumption made in deriving the
conformon equation
simulated in Fig.
11.23
can be stated as follows:
The information (secondary message) required to order amino acid residues in space and
time to produce conformons within an enzyme cannot be greater than the amount of the
genetic information (primary message) encoded in the primary structure of the enzyme.
(11.23)
Statement 11.23, if proven to be true, may be referred to as the
Principle of
Information Conservation Principle
(PIC), in analogy to the
Principle
of
Energy
Conservation
(PEC) in thermodynamics.
