Friday, October 16, 2009

Single Molecule in Sight

A few weeks ago I traveled from my home in Fort Collins down to Golden, Colorado to hear Vladamir Lunin from the Institute of Mathematical Problems of Biology in Pushchino, Russia give a lecture on x-ray crystallography at the the National Renewable Energy Lab (NREL). He spoke about how to improve the three dimensional map of a crystal structure by applying Fourier-transforms and other mathematical operations to crystal diffraction data.  Ab initio phasing as it is known.

This was a talk from first principles as Dr. Lunin built the talk from an explanation of electrons and waves all the way to showing the audience 0.8 ångström resolution data. At this high level of resolution one is able to see the shape of electron orbitals of the atoms in the molecule under investigation (you can believe your quantum mechanics teacher - they weren't just making that stuff up). He also showed some images of low density lipoproteins LDLs (which are massive molecules) at low resolution.  This was all very impressive work but I wanted to know what this distinguished crystallographer thought of the so-called intrinsically disordered proteins. The more than 80% of Eukaryotic proteins that are not  "well behaved" in the context of crystallography.

When I asked him how to deal with understanding the structure of these seemingly un-crystalizable proteins he first mentioned NMR as an alternative technique but then quickly said that he thought single molecule investigation was the wave of the future. He was cautious in this assumption saying that these techniques seem to be perpetually "under development" and rarely give a clear picture of what is actually going on.  My mind immediately went back to the spring of 2007 when I took part in a class put on by graduate students as a series of seminars covering different single molecule techniques in biochemistry.  Here I talk about how I first learned of Steven Chu while preparing my talk on optical trapping for this course.  Recently, because of Vladamir's talk and also discussions of this paper appearing in the August 28th issue of Science I have had renewed hope that the large gap in our understanding of biochemical mechanisms between events visible under a microscope and those accessible by crystallography might actually be filled in. As a  prime example look at the incredible resolution achieved by scientists working for IBM in Zurich on visualizing a pentacene molecule.


 


Researchers attached a single molecule of carbon monoxide to the gold tip of the scanning arm of an atomic force microscope and probed the surface of this molecule of carbon and hydrogen.  The angles of the bonds between the carbon are in plain sight and the individual hydrogen atoms are there! Notice the apparent electron density at the outer rims of the two ends of the pentacene.  I wonder if this is a product of the imaging or if the increased density represents slowing electron traffic as they round the turns.

To anyone who has opened up an organic chemistry textbook and thought of the straight black lines as just part of some mad scientist's imagination this image gives us all reason to do a double take and affirm our collective comprehension of the "atomic theory" as a theory based in the real world rather than buried in obscure wave equations. This image amongst many takes the uncertainty out of the "uncertainty principle" and affixes it as a representation of electrons frozen in time.


 
Gross, L., Mohn, F., Moll, N., Liljeroth, P., & Meyer, G. (2009). The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy Science, 325 (5944), 1110-1114 DOI: 10.1126/science.1176210


Lunin, V., Lunina, N., Ritter, S., Frey, I., Berg, A., Diederichs, K., Podjarny, A., Urzhumtsev, A., & Baumstark, M. (2001). Low-resolution data analysis for low-density lipoprotein particle Acta Crystallographica Section D Biological Crystallography, 57 (1), 108-121 DOI: 10.1107/S0907444900014608
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