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Cukier Develops Molecular Dynamics Code to Explore Complex Proteins

Chemistry Professor Robert Cukier uses Statistical Mechanics and Quantum Mechanics to create theories of and carry out simulations on electron (ET), proton (PT) and proton-coupled electron (PCET) transfer, proton translocation, large-scale domain motion of proteins, and enzyme reactions mechanisms.

To facilitate his work, he has developed CUKMODY, a molecular dynamics (MD) code that simulates proteins. CUKMODY helps accelerate the high dimensional configuration space of molecular dynamics – a significant challenge in working with proteins – and couples molecular dynamics to quantum mechanics.

Protein at the Molecular Level

Biological function relies on the chemical reactions of electron and proton transfer that take place in enzyme-active centers. These reactions are strongly influenced by the geometry and energetics of the surrounding medium. The small masses of electrons and protons necessitate a quantum mechanical treatment and, as electrons and protons are charged species, they strongly interact with the many strongly polar amino acids in the surrounding proteins.

A coupling of proton motion to electron transfer is basic to biological energy conversion. Chains of hydrogen bonded water and/or amino acid residues are essential to proton translocation – the movement of protons across membranes to create electrochemical gradients for energy transduction. Cukier has developed methods to treat the protons involved in translocation quantum mechanically and has coupled them to the surrounding protein in order to simulate rates of this process. The methods have been applied to cytochrome c oxidase, an enzyme responsible for converting the energy from redox and oxygen chemistry to support proton translocation and create a transmembrane pH gradient used for ATP production.

– Institute for Cyber-Enabled Research (iCER)

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