Chris Tepedino
Staff Writer

A team of researchers at the university may have solved the riddle to analyzing the molecular structure of proteins and other complex molecules. The answer may be the small chargeless particle known as the neutron.
Throughout the history of biochemistry, certain molecules have been difficult to examine at the atomic level. None have been harder to find and hold more importance than the tiny hydrogen atom.
“Hydrogen atoms are important in catalysts in one substrate to another,” Elizabeth Howell said, a University of Tennessee biochemistry professor and member of the research team. “They can change other (proteins) from activators to inhibitors or from inhibitors to activators.”
The study performed by Howell, UT associate professor of biochemistry Chris Dealwis, graduate student Brad Bennett and other researchers at Los Alamos National Laboratory shows neutrons are capable of finding the elusive hydrogen atoms and revealing the structure of complex molecules.
Conducted at Los Alamos, the study involved firing neutrons at a drug molecule called methotrexate bound with a protein known as dihydrofolate reductase (DHFR). The choice of methotrexate and DHFR was not a coincidence.
“Dihydrofolate reductase is a target for anti-cancer drugs, anti-malarial drugs and anti-bacterial drugs,” Howell said.
Similarly important, methotrexate is used in the treatment of cancer and auto-immune diseases by reversibly inhibiting DHFR and catalyzing the conversion of DHFR to tetrahydrofolate. Analyzing the molecular structure of this important combination was a primary goal of the study.
To turn the protein-bound drug into a solid for the experiment, they transformed it into a crystal by a process called crystallography. A common method of this technique is adding small molecules to a solution until excess space is reduced and a rigid molecular structure forms. This leads to more accurate results during the collisions with neutrons.
Howell used the analogy of a spacious room.
“Take this room — right now I can move around easily,” she said. “But if I add (stuff), it becomes cramped.”
She said the idea is that “the protein has less room to move.”
Using the Los Alamos National Laboratory’s Neutron Scattering Center, neutrons were then shot at high speed into the crystallized protein-bound drug. Only recently has equipment become available that allows for the precise manipulation of neutrons at sites like Los Alamos. Although neutron diffraction is a relatively new science even when compared to quantum mechanics or atomic theory, it has already produced breakthroughs in molecular composition.
Neutrons provide an advantage over other particles for analyzing molecular structure. Their size allows them to interact with tiny matter, and their neutral electric charge limits interactivity with most matter.
“When X-rays hit (a crystallized protein), they are scattered by electrons, which are outside the nucleus,” Dealwis said. “Between neutrons and X-rays, there is a fundamental difference in scattering.”
Neutrons can penetrate to the nucleus of a hydrogen atom. X-rays of a similar wavelength as neutrons become caught up in the electron field of the atom and larger particles have trouble finding the atom because of the atom’s diminutive size.
The neutrons proved successful in the experiment. Mathematical data gathered from the collisions revealed characteristics of how methotrexate and DHFR bind together.
“The importance of the experiment is that it to some degree talks about the dynamics of molecules,” Howell said.
Comparing methotrexate and DHFR to a lock and key, she said, “Before, the lock and key were static, and they had to fit together. Now, we know the lock and key are flexible and can push against one another.”
The success of the experiment bodes well for other scientists who wish to conduct similar research at Oak Ridge’s Spallation Neutron Source. At maximum capacity, the Spallation Neutron Source will be able to produce the most intense pulsed neutron beams in the world.
“It took a month to gather the data at Los Alamos National Laboratory,” Dealwis said. “At the Spallation Neutron Source, it would take two days.”
With more powerful tools, understanding of the molecular structure will improve. One of the byproducts may be more effective medicine to combat feared diseases.
“This is all theoretical,” Dealwis said. “But in the future, better drug molecules will be able to be created.”