From: Hal Finney (hal@finney.org)
Date: Fri Jun 20 2003 - 00:26:49 MDT
Don't know much about biology, but I've been searching out images of
biological macromolecules and nanomachines. I've been trying to get a
feel for how things work at the nanometer to micron scale, for how the
world is. It is in many ways bewilderingly different from our own world,
but there are points of contact.
The Protein Data Bank, http://www.rcsb.org/pdb/, is the main repository
for protein structures. There are a number of free viewers which
can read PDB files and display them interactively. I was able to get
the Chime plug-in to work with an old Netscape browser I still had.
http://www.imm.org/Parts/MolVis.html describes several of the viewers,
and also has links to a few large nanotech designs stored as PDB files.
The PDB has an educational poster that shows a number of important
biomolecules scaled up 3 million times. This makes the atoms just
visible as small dots. The poster shows a cell membrane with several
receptors and channels poking through it; DNA being worked on by various
protein complexes; the ribosome with some of its associated molecules;
actin and myosin fibers, microtubules; antibodies; even a rhinovirus.
They have a small version of the poster online at
http://www.rcsb.org/pdb/molecules/poster_quickref.pdf, and you can request
a big one about 20 by 30 inches if you send a request with your name
and address to info@rcsb.org.
I've got the poster hanging on my wall now, and it's simultaneously
intriguing and frustrating. At this scale a typical 1 micron bacterium
would be about 3 meters in diameter; maybe the size of a bus. There's
room for lots and lots of complexity at the scale we are looking at
in these pictures. The frustrating part is that it is so hard to tell
what anything does, just by looking at it. Some things do make sense,
the cell channels, the fibers, maybe some of the DNA machines. But the
ribosome is a total mystery, it's just a couple of blobs. And with
the small molecules there's no way to tell what's a poison and what's
absolutely crucial to life.
I found another web site with some amazing graphics of the bacterial
flagellum. This is the corkscrew-shaped "propeller" that sticks out
of some kinds of bacteria and spins to move it along through the water.
The flagellar motor is interesting in itself, but this site focuses on
how the flagella are assembled. They are many times longer than the
bacterium itself, and it turns out that they grow outside the bacterium,
growing from the tip. The inside of the flagellum is hollow, and the
main flagellum protein, flagellin or F41, is sent down the tube from
the bacterium until it comes out the hollow end.
The flagellum has 11-fold symmetry, built from repeating units of this
flagellin protein in a spiral pattern, but at the end there is a cap
with 5-fold symmetry. This means that the cap doesn't fit evenly and
there is one part which is stretched. As the flagellin molecules come
out the end, this asymmetry in the cap acts as a sorting engine and
makes sure they come to rest in the next available spot.
The site has some amazing graphics that make all this very clear. It is
at http://www.npn.jst.go.jp/. Click on the Movies link; they have five
pages which show how the flagellum is organized and then how it is built.
The last one is the most impressive and really sums it all up.
One last site I'll mention is the home page of David Goodsell of Scripps
Institute, http://www.scripps.edu/pub/goodsell/. He has a painting of a
macrophage engulfing a bacterial cell that is incredible in its detail.
At first it just looks like a jumble, but if you read the captions on
some of his other paintings on the site, you can start to pick things
out. It helps to use the PDB PDF file above as a guide for some of it.
It shows how crowded and busy these cells are. It's not just water with
a few impurities.
Goodsell is coming out with a book, Bionanotechnology, Lessons from
Nature. The cover, http://www.scripps.edu/pub/goodsell/books/bionanotech.gif,
shows a DNA molecule passing through a Drexlerian bearing ring. But
the book is really about natural biological nanomachines. His Chapter 1
excerpt begins:
> Nanotechnology is available, today, to anyone with a laboratory and
> imagination. You can create custom nanomachines using commercially
> available kits and reagents. You can design and build nanoscale
> assemblers that synthesize interesting molecules. You can construct
> tiny machines that seek out cancer cells and kill them. You can build
> molecule-size sensors for detecting light, acidity or trace amounts of
> poisonous metals. Nanotechnology is a reality today, and nanotechnology
> is accessible with remarkably modest resources.
Sounds like a must-read book! BTW I've ordered volume 2 of Robert
Freitas' Nanomedicine, but it has been delayed from its May shipping date.
I think they're saying July now. I'll try to provide a review once I
receive it.
Hal
This archive was generated by hypermail 2.1.5 : Fri Jun 20 2003 - 01:01:45 MDT
