The Problem with Protein Folding

Unscattering

Nearly every animal uses electromagnetic radiation to make sense of its environment. The human eye, for instance, detects (and the brain interprets) photons of visible light that are constantly absorbed and reemitted by the things around us, giving us a picture of our world.

With sophisticated systems of lenses for magnification, we can see light reflected from objects as small as 200 nanometers (nm) across, but no smaller. Why? Is it simply our inability to build a better light microscope, or something more fundamental?

In fact, there is something more fundamental at work. The equation well-known to physicists as Bragg's Law states that when we view things using electromagnetic radiation, the smallest object we can see measures one half the wavelength of the radiation used. Visible light has wavelengths ranging from approximately 400 to 750 nm, so the theoretical upper limit on resolution is (400 nm / 2) = 200 nm.

A light microscope is therefore useless to the chemist trying to determine molecular structure, where resolution on the order of bond lengths (0.150 nm) is necessary. Instead they use X-rays, whose wavelengths vary from 10 to 0.01 nm, in a technique known as X-ray crystallography. Chemists first grow crystals of the substance to be studied. The crystals are necessary, because the repeating units found in crystals amplify the diffraction of the X-rays enough to allow computers to interpret it. As the crystal is rotated through 360 degrees, two-dimensional diffraction patterns are generated at each step of the way.

In the end, a computer takes the raw data from these patterns and creates a three-dimensional electron-density map, which is then fitted with a theoretical model of the molecule. This shows how closely theory and experiment can be intertwined in science!

Freeze, You're on Candid Camera: Many molecular biologists freeze dry samples of a protein and study its molecular structure with imaging technologies such as X-ray crystallography and NMR. These researchers are hoping to find average conformations, typical shapes for the molecule. Computers are an important part of the imaging system. They make sense out of very fuzzy electron density patterns captured during the process and turn them into 3D representations of the molecules in the samples. The imaging process takes the activity and the influence of the fluid out of the equation. Somehow this has to be factored back in by the computers processing the information.