Research intended to answer question of how bacteria tackle pollutants, and will involve collaboration with Whitman student researchers

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WALLA WALLA – Supported by a National Science Foundation (NSF) grant, Tim Machonkin, a Whitman College assistant professor of chemistry, is working to understand how bacteria have evolved the ability to neutralize the effects of certain chlorinated organic molecules that are dangerous pollutants in the environment.

The three-year $259,000 grant will enable him to pursue further research designed to unlock the mystery of how certain enzymes can bind to these chlorinated molecules and carry out chemical transformations.

Finding an answer could result in the future development of engineered enzymes capable of neutralizing pollutants such as PCBs, Machonkin explained.

NSF funds only the projects it thinks will work. “This National Science Foundation grant is a significant indicator of the caliber of Whitman’s science faculty as well as the research its members conduct,” said Timothy Kaufman-Osborn, Whitman’s provost and dean of the faculty.

“Professor Machonkin’s grant is especially intriguing because it involves a collaboration with a large research university. Whitman students will spend summers working with graduate students at the University of Rochester, and that will provide them a wonderful opportunity to get a sense of what is involved in doing graduate work in chemistry."

He said the preliminary data that convinced NSF to fund the project was developed in part through the “heavy involvement” of six Whitman students who collectively have spent “hundreds of hours” in the lab. This project also has resulted in “very high exposure” for students who have presented data at past national chemistry conferences, he said.

Machonkin said scientists know from past attempts that trying to use bacteria to neutralize PCBs fails largely because a key enzyme in the process dies when coming into contact with chlorinated molecules.

Machonkin
Tim Machonkin

But his research is focusing on a somewhat ignored enzyme, PcpA, which could bring about a solution.

He said it has been documented that a certain species of bacterium successfully neutralizes a different pollutant, pentachlorophenol, a pesticide used as a wood preservative for telephone poles and railroad ties and such. The bacteria are able to use pentachlorophenol as a food source, breaking the pesticide down into carbon dioxide and water. One of the enzymes the bacteria use is called PcpA. And unlike related enzymes that were killed by chlorinated molecules when previous research tried to use them for PCB removal, PcpA prefers chlorinated molecules.

Machonkin said the existence of PcpA was documented in 1999 in published papers. But since its discovery nothing has been done, and he said there should be research because this enzyme is “doing chemistry that no other enzyme can do.”

If Machonkin and his students can solve how PcpA successfully works on chlorine molecules, the results would pave the way for the engineering of enzymes with the novel properties needed to neutralize other pollutants.

Scientists understand what happens when these enzymes get killed by chlorinated molecules, but they don’t understand why, he said. “If we don’t understand why, we can’t fix the problem.”

He said this enzyme appears to have evolved recently to degrade synthetic compounds that entered the environment through human activity.

Machonkin speculated that “nature never had an enzyme that did this” until 70 years ago — after the development and use of pentachlorophenol. “Nature has done something interesting; it’s just a question for us to figure out.”

Past students involved in this research were HongNgoc Pham ’08, chemistry major, now pursing a doctorate in chemistry at the University of Wisconsin; Justin Liberman ’08, a chemistry major, now a med student at University of Arizona.

Current student researchers include Kristine Smith ’10, who will pursue a doctorate in chemistry at the University of Wisconsin; Amy Doerner ’10, who will pursue a doctorate in chemistry at Yale University; Anees Daud ’10, who is applying to medical school; and Paul DaRosa '10, who is taking a year off in advance of graduate school intentions.

The NSF grant will enable Machonkin to collaborate with up to four student researchers per year. The newest researcher on board is Johnny Zimmerman '11, a chemistry major, who is set to conduct research this summer.