Purdue physicists put new perspective on biochemical problem
The structure of the methane monooxygenase reaction intermediate predicted by Purdue associate professor of physics Jorge H. Rodriguez and his former graduate student Teepanis Chachiyo. (Image courtesy of Jorge H. Rodriguez)
WEST LAFAYETTE, Ind. — Purdue University physicists created computational tools that can predict the fleeting structures of iron-containing enzymes as they transform during chemical reactions. Many of these temporary but critical structures have eluded capture through traditional experimental methods such as X-ray crystallography.
Jorge H. Rodriguez, associate professor of physics, has used computational quantum mechanics to model such structures, called reaction intermediates. He calls this combination of biochemistry and quantum physics "quantum biochemistry."
"The quantum mechanical laws of nature that govern materials - which have been extensively studied in condensed matter physics - also govern the behavior of biochemical systems," Rodriguez said. "During biochemical reactions it is actually the interactions of electrons - tiny particles within atoms - that largely dictates the efficiency and rate at which these reactions occur."
By carefully tracking and calculating the electron interactions, one can predict many physical and chemical properties of molecules, including their geometric structures. The method has the potential to determine the structural changes a biological molecule undergoes and the intermediates formed during the reaction process, he said.
Rodriguez and his former graduate student Teepanis Chachiyo recently predicted the structure of a reaction intermediate of the enzyme methane monooxygenase as it spurs the conversion of methane into the alternative fuel source methanol.
"Knowing the structure of a key reaction intermediate in the methane to methanol reaction greatly helps in understanding the process and may help with laboratory replication of the catalytic cycle of the enzyme," Rodriguez said.
The computational procedure and structure of the methane monooxygenase intermediate are detailed in a paper in the Dec. 22 issue of the Royal Society of Chemistry journal Dalton Transactions. This research was funded in part by a National Science Foundation CAREER award to Rodriguez.
Large biological molecules have clouds of many electrons whirling around them, and it had been difficult in the past to accurately calculate and keep track of so many electron-electron interactions, he said.
Rodriguez and Chachiyo used algorithms run on powerful parallel-processing computers that can compute key physical and chemical properties of iron-containing enzymes. They also incorporated experimental information obtained through a technique known as iron-57 Mössbauer spectroscopy. Their methods include algorithms that accurately predict iron-57 spectroscopic parameters and can predict geometric structures that are compatible with those parameters. The team also performed computational analysis of other experimental techniques, including optical spectroscopy, to further validate their results, Rodriguez said.
Many metal-containing enzymes, called metalloproteins, act as catalysts to accelerate the rate of important biochemical reactions and are of scientific interest. Rodriguez also chose to focus on metalloproteins because areas within these molecules undergo changes in their magnetism during reactions with other molecules, such as oxygen, based on changes in a property of electrons called "spin." Electrons can spin in two directions, up or down. When electrons centered on the metals line up in certain patterns of up and down spins, the part of the molecule involved in the reaction becomes magnetically ordered.
The concept of magnetic transitions has been studied extensively in physics, but traditionally has only been looked at in solid-state materials. The understanding that changes in the spin states influence molecular function as they go through each step of a biochemical reaction had not been explored much in biochemical research, Rodriguez said.
"Theoretical physicists may use experimental information to understand at a fundamental level why certain biochemical processes happen, and this is complementary to the work of biochemists," Rodriguez said. "Biochemists have already observed and understood many aspects of catalytic processes, but we can take that understanding to a deeper atomic-scale level. The kinds of computational methods we use and develop open the door for predictions in an area of science where we had previously only been able to describe what happened after experimental observation."
Rodriguez next plans to apply his methodology to other important biochemical reactions catalyzed by iron-containing enzymes.
"There is an entire class of metal-containing enzymes for which there is no structural information about their reaction intermediates," he said. "With our methodology in place, as long as we have spectroscopic information we can potentially predict these intermediate structures that may otherwise be unattainable."
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Structure, Electronic Configuration, and Mössbauer Spectral Parameters of an Antiferromagnetic Fe2-peroxo Intermediate of Methane Monooxygenase
Teepanis Chachiyo and Jorge H. Rodriguez
Determining the structures of reaction intermediates is crucial for understanding catalytic cycles of metalloenzymes. However, short life times or experimental difficulties have prevented obtaining such structures for many enzymes of interest. We report geometric and electronic structures of a peroxo intermediate in the catalytic cycle of methane monooxygenase hydroxylase (MMOH) for which there is no crystallographic characterization. The structure was predicted via spin density functional theory using 57Fe Mössbauer spectral parameters as a reference. Computed isomer shifts (∂Fe=+0.68, +0.66 mm/s) and quadrupole splittings (ΔΕQ=-1.49, -1.48 mm/s) for the predicted structure are in excellent agreement with experimental values of a peroxo MMOH intermediate. Predicted peroxo to iron charge transfer bands agree with UV-Vis spectroscopy. Peroxide binds in a cis μ-1,2 fashion and plays a dominant role in the active site's electronic structure. This induces a ferromagnetic to antiferromagnetic transition of the diiron core weakening the O-O bond in preparation for cleavage in subsequent steps of the catalytic cycle.