Cracking the structural mystery
"There are many different examples of directed evolution being used to produce catalysts that enhance the speed of commercial or synthetic processes, but the fact that you have a good catalyst doesn't give you any information about how it works," Houk said.
To determine the molecular structures of both LovD and LovD9, Yeates' laboratory grew protein crystals from each enzyme and scattered X-rays off of them in a process called X-ray crystallography. These measurements gave Yeates an in-depth look at the molecular architecture of the enzymes, yet both appeared virtually identical, with no obvious structural variations to explain why LovD9 was more efficient.
While the two enzymes might appear similar when in solid crystal form, they behave quite differently when immersed in water, Houk said. The enzymes are composed of long chains of amino acids that can rotate and twist when allowed to move freely, yet this complex motion cannot be easily observed through laboratory experiments.
To quantify these minute molecular fluctuations, Houk and Jimnez-Oss used a computer program that simulates how the mutated and natural enzymes undergo internal motions when dissolved in water, and how this motion will influence the ability of the enzymes to cause the transformation that synthesizes simvastatin.
Determining why the mutated LovD9 enzyme works better than its natural counterpart involved simulating the movement of the complex enzyme in a fluid environment over a period just microseconds long. A microsecond may seem like a very short amount of time, but computations for the motion of such a large molecule required massive computing resources, Houk said.
The team was able to harness the tremendous amount of computing power necessary for these calculations by using the National Science Foundationsponsored Anton supercomputer designed by the D. E. Shaw Research laboratory
|Contact: Stuart Wolpert|
University of California - Los Angeles