The Bommarius lab seeks undergraduate students interested in challenging research!
The Bommarius laboratory (ChBE, CHEM, Bioengineering) specializes in biocatalysis, green
chemistry, protein stability, and biochemical engineering. We seek self-motivated, hard-working
student researchers interested to continue for a PhD and/or MD after college, to work on cuttingedge
research problems and to learn new skills.
Eligibility:
i) graduation date (B.S.) between 05/18 and 12/19 in BIOL, ChBE, or CHEM
ii) GPA at Georgia Tech > 3.30, preferably > 3.5
iii) basic laboratory skills, enthusiasm, self-motivation, flexibility, independence
iv) start in Fall 2017 for credit, continuation during spring, summer possible and expected
Interested? Please email resume (incl. i) major, ii) GPA, and iii) expected graduation date) to
mentor and to Prof. Andreas S. Bommarius (andreas [dot] bommarius [at] chbe [dot] gatech [dot] edu).
Interviews with mentor: any time; feedback: less than 1 day later; decision asap after
agreement among student, mentor, and faculty advisor
1. Study of an antibiotic-producing enzyme - Mentor: Matt McDonald
Beta-lactam antibiotics are the most used antibiotics in the world. Synthesis of betalactam antibiotics via enzyme catalysis provides an eco-friendly path to meet demand. In this study, penicillin G acylase (PGA) is used to produce ampicillin. To move to continuous production, the lifetime of the catalyst must be known. This study aims to understand the mechanism of PGA deactivation over time as a function of temperature. Several proposed mechanisms can describe our preliminary results, the goal of this project is to narrow the number of possible models until the true mechanism is known or a new mechanism is uncovered. Three variants of PGA will be examined to see if mutants with improved catalytic activity also have adequate stability. This project therefore has two parts:
Cloning and production of PGA variants in E. coli
Elucidation of enzyme deactivation mechanism
Interested students may come from varied majors, such as BCHM and ChBE and should be comfortable with basic laboratory skills, such as pipetting or titrating. PGA does not express well in E. coli, therefore the first part of this project will be challenging; applicants should be familiar with cloning (the theory behind it and the patience to follow complex directions) to expedite this step. Students can expect to learn about the entire protein production process, from manipulating DNA, to expression, to protein purification. Afterproducing the enzyme, the catalytic activity will be assessed for stability in batches and a continuous enzyme membrane reactor (EMR). Analysis of this data requires model fitting, therefore students should be familiar with MATLAB and can expect to learn about enzyme kinetics, deactivation kinetics, and model discrimination. Polarimetry will be used to measure enzyme kinetics.
2. Investigating protein stability of an amine dehydrogenase - Mentor: Dr. Bettina Bommarius
Amine dehydrogenases are newly developed enzymes in the Bommarius lab used in the production of chiral amines, which are essential in the pharmaceutical industry. With the correct enantiomer, specific pharmaceutical products can be used for applications such as stimulants, vasoconstrictors, decongestants, antihistamines, and antidepressants. Producing the enantiomerically pure product is essential in this industry because they lead to lower dosage amounts and limit possible side effects of the drug being made. The amine dehydrogenases the Bommarius lab has developed based on an amino acid scaffold are L-AmDH, (derived from leucine dehydrogenase), F-AmDH (derived from phenylalanine dehydrogenase), and a chimeric amine dehydrogenase combining the previous two enzymes (cFL1-AmDH). These enzymes catalyze the reduction of ketones to the corresponding chiral amines, a biocatalyst route that is beneficial to the development of active pharmaceutical ingredients (API) compared to the established chemical route, which is inferior in enantiomeric purity, chemical waste and yield.
While enzymes in general perform with outstanding enantiomeric excess, their stability in other than mild aqueous solutions is often poor. We are seeking to improve the enzyme stability towards operational conditions that make these amine dehydrogenases suitable for pharmaceutical applications. The protein is available already expressed in large amounts and after initial stability data was obtained further protein engineering is required. The overarching design goal for the fall semester is to engineer the amine dehydrogenases to be reasonably active in 5 M ammonia, ionic strength of 5 M, and 60% acetonitrile in solution. Using an established error-prone PCR strategy (EP-PCR) with an established high-throughput activity assay, we will engineer amine dehydrogenases that are reasonably functional (i.e., an activity of 6 U/mg) in 5 M ammonia, ionic strength of 5 M and 60% acetonitrile in solution. The evolution of two amine dehydrogenases cFL1-AmDH and F-AmDH will be accomplished via a stepwise strategy, in which we will randomly modify either gene via EP-PCR at any intermediate set of milieu conditions (e.g., in 3 M ammonia, ionic strength of 3 M and 40% acetonitrile in solution), in tandem with a functional screen.