Modeling and Optimization in Directed Evolution Protocols and Protein Engineering

Open Access
Moore, Gregory Lee
Graduate Program:
Chemical Engineering
Doctor of Philosophy
Document Type:
Date of Defense:
March 01, 2005
Committee Members:
  • Costas D Maranas, Committee Chair
  • Ali Borhan, Committee Member
  • Patrick Cirino, Committee Member
  • Stephen James Benkovic, Committee Member
  • Andrew Zydney, Committee Member
  • directed evolution
  • protein engineering
  • optimization
The central theme of this thesis aims toward the systematic development of integrated approaches for proactively designing protein libraries with focused diversity for directed evolution and protein engineering experiments. Experimental paradigms for library generation rely on the generation of point mutations, recombination of parental sequence segments, and ab initio library design using degenerate oligonucleotides. In response to these library design paradigms, this thesis presents a computational toolbox for quantifying how diversity is generated and allocated in the combinatorial DNA library and what sequence permutations are the most promising in terms of preserving protein structure and activity.