Molecular recognition

Dear Colleagues,

As Pedro noted, existing approach for description of molecular recognition
phenomena basically goes for the classic views. The "key-lock" model
continues in development of more sophisticated views, but actually they are
similar to this initial model. Analysing the basis of biomolecular
specificity and affinity, we ultimately come to the quantum picture. What we
need is to show that quantum approach can give some unexpected understanding
that is absent in the classical approach. Here I will try to outline some
moments.

The duration of the elementary action of the chemical reaction is somewhat
between ten to minus 15 or minus 12 seconds. During enzymatic catalysis,
this is the time of initial interaction but the whole process is slower by
10-15 orders of magnitude and may take seconds (for slow enzymes). The order
of magnitude between the duration of human life and the time from Big Bang
is only 8. We usually say that biomolecules increase the rates of reactions
but they operate slowly. Really they make possible the routes that much less
probable without them are realize them with high precision. And they pay for
this precision by slow turnovers. We see that recognition organizes time
scale.

What enzymes are fast and what are slow? Fast enzymes catalyse reactions in
microseconds (e.g. carbonic anhydrase, catalase) while slow enzymes - in
seconds. If we look at the reactions, we will see that fast enzymes catalyse
steps that easily occur in the absence of catalyst, while slow enzymes
catalyse very complex steps that are almost not probable in the nature.
According to Pedro, enzymes are molecular automata and it is true that they
are quantum automata. They actually select states (or better to say -
routes) from the set of possible alternative realizations at the quantum
level.

I think that for quantum approach in understanding molecular recognition,
some proteins catching bosons (photons) and responding by fermions circuits
(electron-proton separation) can be useful. E.g. for bacteriorodopsin the
duration of each step of its conformational movement is precisely
determined, and some steps differ drastically in time. Enzyme should also
exchange bosons with substrate molecules. The time of measurement includes
holding of coherent event during measurement, thus dissipation of energy is
minimal. This is the reason for stability and reliability of living process
in macroscopic time. Internal circuits and oscillations within measuring
device are predicted by quantum measurement model of Braginsky (references
in my papers below) and in recent developments of quantum computation
models. The uncertainty between measurement of energy of the system and time
of its observation is expressed via Heisenberg's energy-time uncertainty
ratio and increasing time of measurement decreases uncertainty in energy
that means definitiveness of selection of a certain route. Actual time of
measurement corresponds to (selectively valid) equilibration between
reliability and flexibility of the system in its surrounding.

I started to develop this approach (which arises to ideas of Howard Pattee,
Robert Rosen and Michael Conrad) in my paper in BioSystems in 1993 (or from
1985 in papers in Russian). You can find details in:

Igamberdiev AU (1993) Quantum mechanical properties of biosystems - a
framework for complexity, structural stability, and transformations.
BioSystems 31 (1): 65-73

Igamberdiev AU (1999) Foundations of metabolic organization: coherence as a
basis of computational properties in metabolic networks. BioSystems 50 (1):
1-16

Another example for quantum model is the model of coherence in microtubules
of Hameroff and Penrose for explanation of conscious events. It may
represent a particular case of quantum non-demolition model for molecular
recognitions. It substantiates parallelism of metal and physical events,
which is definitely absent in the classical models of brain operation. The
coherence in microtubules should be the same phenomenon as the coherence
during conformational relaxation of enzymes.

I think what is needed is working out strong physical models underlying
quantum recognition process for molecular interactions and catalysis. This
may correspond to the development of quantum computation paradigm and its
application to living systems. I am sure that necessary background for this
is already present in modern science. Among many things it will explain:

- duration times of conformational processes
- stability and transformations of metabolic networks
- brain operation

Best regards,
Andrei Igamberdiev
Received on Sun May 26 17:28:48 2002