First online models of biological molecules

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A University of Massachusetts Amherst biochemist is creating the first online models of biological molecules like enzymes and proteins customized to figures in scientific research articles.

Readers can rotate the models to view all sides of the molecule, zoom in on mutations and other sites, and in some cases, watch atoms rearrange during chemical reactions.

Frieda Reichsman of the biochemistry and molecular biology department has a one year contract with the American Chemical Society to produce the first online, interactive 3-D models and animations customized to figures in research papers published in Chemical Biology.

"This is the only venue where this technology is being used to accompany journal articles,” says Reichsman. “Other publications provide links to view 3-D structures, but they are generic, not customized to the author's illustrations.”

Biological macromolecules like proteins and DNA can contain thousands of atoms linked together in a specific order. Researchers often study a mutation or chemical reaction that involves a single site on the molecule. Reichsman's models match the structure figures created by researchers and set them in motion.

How the models are created is a blend of art and science. First Reichsman finds the molecule in a database of over 40,000 macromolecules to retrieve detailed information on the location and orientation in space of every atom. Then she designs the molecule using a scripting language associated with a molecular viewing program called Jmol. The language is designed to understand and manipulate the database files in 3-D.

Reichsman can choose the look and feel of the molecule, use different colors for each type of atom and decide between different representations, including ribbon style and ball and stick views. “I can also dictate the orientation of the molecule in space and design controls that allow the user to select views that reveal the function of the molecule,” says Reichsman. To keep viewers oriented, she frequently animates the transitions between different representations and orientations of the molecules.

Through her company, Molecules in Motion, Reichsman collaborates with UMass Amherst scientists. She works closely with Eric Martz, a professor who is pioneering the creation of software for visualization of large molecules. Free, award-winning software created by Martz is being used worldwide by biochemistry and biology students, educators and researchers, including many at UMass Amherst. Reichsman collaborated with Molly Fitzgerald-Hayes to develop and teach the popular Biochemistry 100 My DNA course, for which she created computer-based instructional multimedia resources. “This technology is an important tool for education as well as research,” says Reichsman.

The first set of online models, published in December 2006, show a small molecule bound to an enzyme required for the HIV virus to multiply. “The small molecule blocks the enzyme's ability to copy the genes of the virus,” says Reichsman. “Derivatives of this small molecule could be the source of new anti-viral drugs that help fight AIDS.” The second set of models, released on March 20, 2007, show an enzyme that modifies a precursor to an antibiotic, rendering it capable of interfering with the internal workings of a bacteria. The 3-D models illustrate a part of the enzyme acting as a lid that opens to accept an unfinished component of the antibiotic and closes to complete its manufacture.

For more information contact Frieda Reichsman at


The opinions expressed here are the views of the writer and do not necessarily reflect the views and opinions of News Medical.
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