TY - JOUR
T1 - Computationally Exploring and Alleviating the Kinetic Bottlenecks of Anaerobic Methane Oxidation
AU - Grisewood, Matthew J.
AU - Ferry, James G.
AU - Maranas, Costas D.
N1 - Funding Information:
Funding was provided by the Advanced Research Projects Agency-Energy (ARPA-E, DE-AR0000431). Additional funding was provided by The Center for Bioenergy Innovation, a U.S. Department of Energy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science (DE-AC05-00OR22725).
Funding Information:
We would like to thank the Penn State Institute for Cyberscience for maintaining the supercomputers that were used to generate designs. We would also like to thank the members of the ARPA-E REMOTE (Reducing Emissions using Methanotrophic Organisms for Transportation Energy) program for their useful conversations. Funding. Funding was provided by the Advanced Research Projects Agency-Energy (ARPA-E, DE-AR0000431). Additional funding was provided by The Center for Bioenergy Innovation, a U.S. Department of Energy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science (DE-AC05-00OR22725).
Publisher Copyright:
© Copyright © 2018 Grisewood, Ferry and Maranas.
PY - 2018/7/27
Y1 - 2018/7/27
N2 - The anaerobic oxidation of methane (AOM) by methanotrophic archaea offers a carbon- and electron- efficient route for the production of acetate, which can be further processed to yield liquid fuels. This acetate production pathway is initiated by methyl-coenzyme M reductase, but this enzyme can only oxidize trace amounts of methane ex situ. Efforts to improve the kinetics of methyl-coenzyme M reductase through enzyme engineering have been, in part, limited by low-throughput assays. Computational enzyme engineering can circumvent this limitation through the design of smaller, more focused libraries, which have a higher probability of success. By drawing from a new consensus reaction mechanism for Mcr and newly published data, the first complete kinetic characterization of the Mcr reaction mechanism is proposed. In the developed kinetic description, the rate of methyl-coenzyme M unbinding is proposed to limit Mcr overall kinetics. A revised computational method was devised to improve the rate of product release while not disrupting the reaction's activated complex. Large, hydrophobic amino acids that can assume multiple conformations were predicted to be most effective at reaching this design goal. Other rate-limiting scenarios were examined, such as (i) high-temperature (>45°C), (ii) methyltransferase-limiting, and (iii) ineffective cofactor F430 binding. A separate library of designs is put forth for each one of these cases. These efforts mark the first computational attempt at redesigning methyl-coenzyme M reductase for reversed or improved activity, which if experimentally validated, would have a cross-cutting impact across the biotechnology and biochemistry fields by debottlenecking anaerobic methane oxidation.
AB - The anaerobic oxidation of methane (AOM) by methanotrophic archaea offers a carbon- and electron- efficient route for the production of acetate, which can be further processed to yield liquid fuels. This acetate production pathway is initiated by methyl-coenzyme M reductase, but this enzyme can only oxidize trace amounts of methane ex situ. Efforts to improve the kinetics of methyl-coenzyme M reductase through enzyme engineering have been, in part, limited by low-throughput assays. Computational enzyme engineering can circumvent this limitation through the design of smaller, more focused libraries, which have a higher probability of success. By drawing from a new consensus reaction mechanism for Mcr and newly published data, the first complete kinetic characterization of the Mcr reaction mechanism is proposed. In the developed kinetic description, the rate of methyl-coenzyme M unbinding is proposed to limit Mcr overall kinetics. A revised computational method was devised to improve the rate of product release while not disrupting the reaction's activated complex. Large, hydrophobic amino acids that can assume multiple conformations were predicted to be most effective at reaching this design goal. Other rate-limiting scenarios were examined, such as (i) high-temperature (>45°C), (ii) methyltransferase-limiting, and (iii) ineffective cofactor F430 binding. A separate library of designs is put forth for each one of these cases. These efforts mark the first computational attempt at redesigning methyl-coenzyme M reductase for reversed or improved activity, which if experimentally validated, would have a cross-cutting impact across the biotechnology and biochemistry fields by debottlenecking anaerobic methane oxidation.
UR - http://www.scopus.com/inward/record.url?scp=85057261515&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85057261515&partnerID=8YFLogxK
U2 - 10.3389/fenvs.2018.00084
DO - 10.3389/fenvs.2018.00084
M3 - Article
AN - SCOPUS:85057261515
VL - 6
JO - Frontiers in Environmental Science
JF - Frontiers in Environmental Science
SN - 2296-665X
M1 - 84
ER -