X-Message-Number: 17645
From: 
Date: Sat, 22 Sep 2001 04:10:33 EDT
Subject: Allosteric Proteins--One of Our Own BioNano Machines

CryoNet:

Reading K. Eric Drexler's article in the September Issue of "Scientific 
American" magazine gave me the idea to write the following which is based on 
my accumulating knowledge of molecular biology.  To my understanding, it is 
pretty accurate while admittedly hard to read--kind of tough to write too.  
In the Eric's article, he says the following (which is followed by my piece):

QUOTE:
"Decades of technological progress have shrunk microelectronics to the 
threshold of the molecular scale, while scientific progress at the molecular 
level--especially on the molecular machinery of living systems--has now made 
clear to many what was envisioned by a sole genius so long ago [Feynman]."
UNQUOTE

Actually we each already have working nanotechnologies--always have.  It's in 
every cell in our bodies many times over.  My current favorites, from 
innumerable candidates including cellular nanomotors with armatures and 
rotating shafts, are the ubiquitous and super-varied, macromolecular 
*allosteric proteins* (i.e., types of cellular enzymes).  On command (per 
chemical signals--the attaching of atomic ions, or small ionic compounds to a 
specific site on the protein), these huge molecules subtly, or very 
radically, change their three dimensional shapes to instantly reveal 
chemically active sites (i.e., construction or machining sites) previously 
"hidden" in their interiors; or alternatively, momentarily create such sites 
via instantaneous surface alterations compelled by the chemical signal which 
performs as a tiny electromechanical switch.  These chemically active sites 
are then used to help buildup or adapt other manufactured molecules 
(including, I believe, different and newly developing allosteric proteins) 
atom by atom (or mini-molecule by mini-molecule)--sometimes to be handed off 
to other protein machines in a given molecular post-assemby line.  The 
allosteric change (i.e., a twisting and contorting) in this enzymatic protein 
sometimes includes the formation of magnetic (or covalent) vicegrips to hold 
and position specific captured substrates (i.e., a molecules to be modified 
or combined) for a nearby, simultaneously created molecular welding 
site--complete with energy/heat generating apparatus (powered by surrounding 
phosphate-based molecular fuel) for the actual work/modification.  Allosteric 
proteins may stay in their activated state for a while (i.e., many 
nanoseconds) quickly/instantly turning out one finished (or semifinished) 
product after another, or, via a change in their immediate cellular 
environment (sometimes caused/controlled by the increasing number of the 
product itself)--which expells/disconnects the atomic switch--flip back to 
their original three dimensional conformation (i.e., shape)--prepared to do 
it all again on request via attachment of a new signal (i.e., another 
identical electromechanical switch/ion).

The normal three dimensional states of the various allosteric proteins (while 
off-duty and free floating in the cell's enormous volumes of cytoplasm), as 
well as their action figure stances, are absolutely predetermined via 
blueprint from the very beginning from precise recipes drawing from available 
(i.e., floating around) amino acids (i.e., premanufactured building blocks).  
Like all proteins, these massive molecules are first formed block by block 
into one super-long, single dimensional chain known as a polypeptide.  As 
they are turned out from the original factory (truly massive manufacturing 
plants within, or associated with, intracellular organelles), each precisely 
folds-up into its individual species' standard, three dimensional shape like 
a stretched, single-stranded section of rubber band being released after both 
ends have been very tightly twisted in opposite directions.  Unlike the 
rubber band model, the precise balling-up/contorting of the linear molecular 
chain is entirely due to various degrees of predictable magnetic attractions 
and repulsions between its building block/peptide parts (some amino acids are 
charge negative, some positive and some neutral).  In the cellular 
environment, including a near 98.6 degree temperature, allosteric proteins 
form the most sensitive and precarious high tension balancing act between two 
greatly differing three dimensional conformations whereby the tiniest shift 
in net charge at a specific site on the surface of the giant molecule can and 
will be the straw that contorts the camel's back--with an immediate 
re-contorting when the charge is removed.  The magic site on the allosteric 
protein is inaccessible to all but just the right size and shape key with 
just the right charge--the atomic switch.  As with all proteins, during the 
initial three dimensional formulation from a single dimensional chain, 
special monitoring macromolecules/proteins linger close by to assist and to 
see that a new protein's folding proceeds correctly, and if not, to assist in 
its refolding or show it the door (the molecular trash bin).  Properly folded 
(i.e., precisely twisted and contorted), it is now ready for cellular 
service, or ready for modification first by other BioNano Machines--other 
allosteric proteins.

David C. Johnson

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