Katherine E. Liu

Methane Monooxygenase: Models and Mechanism

There is much current interest in non-heme diiron carboxylate proteins. Included are the hydroxylase enzyme of methane monooxygenase (MMO), hemerythrin, ribonucleotide reductase, and purple acid phosphatase, all of which contain a dinuclear iron center at their active site. We ultimately desire an understanding of how these units are tuned in each protein to exhibit diverse functions ranging from the reversible binding of dioxygen in hemerythrin to activation of dioxygen for converting methane to methanol in MMO. In pursuit of this objective, we are investigating the proteins of the MMO system and exploring the fundamental chemistry of the hydroxylase diiron center. In the present article we review some of our recent progress in this area.

Deep Inference for Covariance Estimation: Learning Gaussian Noise Models for State Estimation

We present a novel method of measurement covariance estimation that models measurement uncertainty as a function of the measurement itself. Existing work in predictive sensor modeling outperforms conventional fixed models, but requires domain knowledge of the sensors that heavily influences the accuracy and the computational cost of the models. In this work, we introduce Deep Inference for Covariance Estimation (DICE), which utilizes a deep neural network to predict the covariance of a sensor measurement from raw sensor data. We show that given pairs of raw sensor measurement and ground-truth measurement error, we can learn a representation of the measurement model via supervised regression on the prediction performance of the model, eliminating the need for hand-coded features and parametric forms. Our approach is sensor-agnostic, and we demonstrate improved covariance prediction on both simulated and real data.

From the Mass Production of Methylococcus Capsulatus to the Efficient Separation and Isolation of Methane Monooxygenase Proteins. Characterization of Novel Intermediates in Substrate Reactions of Methane Monooxygenase

Methanotrophs are naturally occurring bacteria which utilize methane as their sole source of metabolic energy and carbon.* Due to their ability to catalyze the formation of methanol from methane under ambient conditions, interest has developed over their use as alternative methanol producers.2 In addition, the fact that they oxidize a variety of hydrocarbon substrates other than methane, attracted a lot of attention in their potential exploitation in bioremediation.3 The metalloenzyme system responsible for the conversion of methane to methanol (Reaction 1) in the initial step of their metabolism is methane monooxygenase (MMO).