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 Rate This Message: http://www.cryonet.org/cgi-bin/rate.cgi?msg=17645