Engineering - Molecular Theory of the Living Cell - page 117

Table 5.1 Enzymes as self-organizing soft-state nanotransistors. Important items are highlighted

Solid-state transistor
(artificial transistor) Soft-state transistor (natural transistor)

1. Process Conducts electricity when

energized

Catalyzes chemical reactions when
energized by substrate binding

Microns (10 6 m) Nanometers (10 9 m) 2. Size

3. Mechanical
property

Rigid (thermally immobile) Deformable/soft (thermally

fluctuating)

4. Field of study Solid-state physics “Soft-state physics,” i.e., enzymology

5. Mechanism of
energization

Current or voltage applied
to gate

Substrate-binding-induced activation
of conformational substates of
Frauenfelder et al. (2001)

6. Terminals Input (source, emitter) Reactants

Trigger (gate, base) Enzyme

Output (drain, collector) Products

10 5 electrons per switching
event (mega-electron
transistor)

7. Electron flow One electron per switching event

(single-electron transistor)

Static and artificially
organized
(covalent bonds,
50-100 kcal/mol)

Dynamic and self-organizing
(Sect. 3.1 ) (noncovalent bonds,
1-5 kcal/mol)

8. Component
connection

9. Mobile objects Electrons Molecules

Holes Ions

Phonons Conformons (Chap. 8 )

10. Number of units
in a logical gate

~20 1 ~ 50

~10 11 ~10 9 11. Number of units

in a processor

12. Behavior Deterministic (binary,

crisp logic)

Nondeterministic (multivalued, fuzzy
logic)

3. Deformability . Traditional transistors are rigid and large enough to resist the
randomizing effects of thermal motions of the structural components of a
transistor. Enzymes are flexible (i.e., soft) and small enough to undergo thermal
fluctuations or Brownian motions that are essential for their functions (Ji 1974a,
1991) (Row 3). This is why enzymes can be viewed as “soft-state transistors,”
the study of which may be referred to as “soft-state physics” (e.g., enzymology)
in contrast to solid-state physics. Examples of soft-state physics include the
study of protein folding, single-molecule enzymology (Xie and Lu (1999);
2001), the informatics of biopolymers, and artificial polymers with mechanically
activatable chemical moieties (Lenhardt et al. 2010).
4. Self-organizing circuits . Solid-state transistors are fabricated by humans, while
soft-state transistors have resulted from spontaneous chemical reaction-diffusion
processes or self-organizing processes (Prigogine 1977, 1980) selected by
biological evolution. The principle of self-organization is rooted in (1) the
dissipation of free energy and (2) the principle of structural complementarity as
exemplified by the Watson-Crick base pairing and the enzyme-substrate complex