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Computational Enzyme Design


Sosa Padilla Araujo, Bernardo (2014) Computational Enzyme Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9KP805N.


Computational protein design (CPD) is the automated identification of amino acid sequences that will fold into a specified three-dimensional structure. This method has emerged as a promising tool for engineering enzymes. In this thesis, I describe my efforts at improving and applying CPD methods to the design of enzymes.

Chapter II describes the development and benchmark results for a molecular dynamics (MD) protocol to prescreen enzyme designs. Results indicate that the MD protocol is successful in screening enzymes for enzymatic activity. The protocol is general, reproducible, and excels at discarding false positive designs while predicting the most active enzymes correctly.

Conformational changes are part of the repertoire that natural enzymes use to catalyze reactions. Chapter III comprises the computational design and experimental characterization of triosephosphate isomerase (TIM), a model enzyme for the study of catalytic activity in the context of conformational changes. Using a novel multi-state design (MSD) method that can consider multiple states in a single protein sequence optimization calculation, we designed the flexible hinges in TIM’s active site loop.

A central challenge in the CPD field is the reliable engineering of an enzyme for any desired reaction. In Chapter IV, I describe the conceptualization and application of a high-throughput computational framework for the de novo design of enzymatic activity into inert scaffolds. TIM is used as a model system.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:computational enzyme design, molecular dynamics, multi-state protein design, de novo enzyme design
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Biochemistry and Molecular Biophysics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Mayo, Stephen L. (advisor)
  • Miller, Thomas F. (co-advisor)
Thesis Committee:
  • Shan, Shu-ou (chair)
  • Mayo, Stephen L.
  • Miller, Thomas F.
  • Clemons, William M.
Defense Date:1 May 2014
Record Number:CaltechTHESIS:05052014-122744794
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8217
Deposited By: Bernardo Sosa Padilla Araujo
Deposited On:21 Mar 2017 18:24
Last Modified:04 Oct 2019 00:04

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