Project Title

Computational Investigations into Biological Stability of Future Naval Fuels

PI

Dr. Anthony M. Dean & Dr. C Mark Maupin

Email

amdean@mines.edu & cmmaupin@mines.edu

Department

Chemical & Biological Engineering

Project summary

This project aims to understand the underlying enzymatic mechanisms that enable microorganisms to metabolize liquid transportation fuel. These micro-organisms employ the benzylsuccinate synthase (BSS) enzyme that uses a stabilized glycyl radical to initiate the metabolism of the hydrocarbon fuel. Free radical chemistry in enzymes is a relatively recent discovery and has been difficult to study experimentally due to the extremely anaerobic conditions in which the enzyme is active. Through the use of ab initio (QM/MM) and molecular dynamics it will be possible to elucidate the underlying mechanistic details of this enzyme catalyzed reaction. The QM/MM calculations will be used to elucidate the activation barriers and the reaction enthalpies & entropies for the underlying catalytic mechanism thereby illuminating the rate determining step. The QM/MM calculations will also enable the creation of a detailed potential energy surface to which the reactive molecular dynamics simulations will be parameterized (MS-EVB model). We propose to use MS-EVB MD simulations to observe the role of dynamical protein motions on the reaction energetics and entropy. This model will also enable the investigation into the proposed enzyme mechanism and the relative stability of key radical species.

Commercial software

AMBER 12

Gaussian09

Open Source software

None