The University of Massachusetts Amherst
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Seminar: Costas D. Maranas, Pennsylvania State University, “Using Computations to Design Pathways Using de novo Steps””


Tuesday, March 23, 2021 - 11:30am


(will be held via Zoom, contact for a link)


Host: Michael Henson
Metabolism is defined as the full complement of chemical transformations in living systems. Our group has previously introduced a variety of computational tools (i.e., OptKnock, OptForce) for shaping host native metabolism towards various overproduction goals. However, in many biotechnological applications an organism metabolic repertoire needs to be expanded upon. To support this goal, we will discuss computational tools for constructing thermodynamically feasible, carbon and energy efficient, overall conversion stoichiometries by globally assessing all possible co-reactant/products combinations. Protein engineering, either de novo or through directed evolution, can expand upon the parts-list available for constructing pathways by re-purposing existing enzymes for novel conversions. However, minimizing the use of novel steps and combining them with existing reactions has remained so far elusive. In response to this unmet need, we developed retrosynthesis tools which allow for seamlessly blending known reactions with de novo steps to construct atom and energy balanced pathways using reaction atom mapping information. We will conclude by offering insight and lessons gained from the application of these tools on a variety of bioproduction challenges.
Costas D. Maranas (b. 1967) is the Donald B. Broughton Professor in the Department of Chemical Engineering at The Pennsylvania State University. He received a Diploma in Chemical Engineering at the Aristotle University, Greece in 1990 and a Ph.D. in Chemical Engineering from Princeton University in 1995. He has been in the faculty of the department of Chemical Engineering at Penn State since 1995. He is the recent recipient of the 2020 Biotechnology Progress Award for Excellence in Biological Engineering Publication and the 2020 International Metabolic Engineering Award. Earlier awards include the Allan P. Colburn Award for Excellence in Publications by a Young Member of AIChE (2002) and the Outstanding Young Investigator Award of the Computing and Systems Technology AIChE Division (2006). Penn State recognitions include the Engineering Alumni Society (PSEAS) Premier (2016) and Outstanding (2012) Research Award. He is a member of a number of journal Editorial Boards including PLOS Computational Biology, BMC Systems Biology, Biotechnology Journal and Metabolic Engineering. He is a Fellow of the American Institute of Chemical Engineers (AIChE) and the American Institute of Medical and Biological Engineering (AIMBE). He is the Lead for the “Use-Inspired Research” in the Center for Bioenergy Innovation (CBI) DOE center, a participant in the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) DOE center, and a member of the leadership team of the NSF Molecular Maker Lab Institute (MMLI).


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