Rice Science Whenever: Map Proteins With X-Rays

How do you classify the active sites of proteins, the bonds which can define whether a cell is cancerous?

X-ray crystallography. The diffraction pattern can tell you the precise 3-D arrangement of every atom in that molecule. If you can get the maths right.

After six years of hard work Jiangpeng Ma‘s team a Rice has gotten the maths right. What this means is that proteins can now be classified, not only chemically but structurally.

More important, the team has mapped an actual protein to its computational system, proving the mathematical model.

Dr. Ma, whose work is shared between Rice and the Baylor College of Medicine, specializes in what he calls "Computational & Experimental
Structural Biology & Cell Biology." That means he examines the structure of cells, using both experimental techniques and mathematics.

This means his work crosses many disciplines, which is an important point to think about in this era of hyper-specialization. His lab is affiliated with the physics, bioengineering and computing labs at Rice, as well as two labs at Baylor.

But as with all things, Dr. Ma did not do this alone.

In the release about the breakthrough, Ma gave credit to Billy Poon,
a Rice graduate student who first came to campus in 2001, and to whom he gave the
original assignment.  (Some Web research indicates Mr. Poon may be a Cornell graduate, but I can’t confirm that.)

"The success of this project is really a story
about Billy’s perseverance and determination," he said. While most
graduate students get publication credit in the increments of a
project, Poon’s project offered a large payoff with no
option for publication until the work was done.

"His fellow students in the
research group published tons of material during the years that he
worked on this," Ma said. "He didn’t have anything to show for his
efforts, and he was under enormous pressure."

Poon eventually created a computer
"map" of a protein, which the team then had to fit to an actual
protein, while only able to see a small portion of it at a time.

Enter Xiaorui Chen, who joined Baylor from Tsinghua University in Beijing (Dr. Ma is a graduate of Fudan University, in Shanghai.) She solved the problem, spending
so many hours at her table wearing special goggles ("googled" in other
words) she learned to eat with the goggles on. The problem was finally
solved at Christmas.

"Nobody was sure it would work out before that, and it’s a rare treat
when a scientist gets to witness a success like this one, which was
pivotal not only for myself and my students but also for every other
scientist in this field."

The job now is to prove the general validity of the methodology,
using membrane proteins, and to design laboratory facilities which will
regularize the categorization work.

Now, what does all this mean?