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Title page for ETD etd-12132013-151025


Type of Document Dissertation
Author Combs, Steven Anthony
Author's Email Address steven.combs1@gmail.com
URN etd-12132013-151025
Title Identification and Scoring of Partial Covalent Interactions in Proteins and Protein Ligand Complexes
Degree PhD
Department Chemistry
Advisory Committee
Advisor Name Title
Jens Meiler Committee Chair
Brian Bachmann Committee Member
Martin Egli Committee Member
Richard Armstrong Committee Member
Keywords
  • protein modeling
  • ligand docking
  • rosetta
  • structural biology
  • computational chemistry
Date of Defense 2013-08-16
Availability unrestricted
Abstract
Partial covalent interactions (PCI) such as hydrogen bonds, salt bridges, cation-π, and π-π interactions contribute to protein thermostability. Algorithms that identify PCIs rely on pairwise atom-atom angles and distances, neglecting that PCIs occur between an electron deficient hydrogen and an electron orbital of the accepting atom. Accurate chemical representation of PCIs will improve protein thermostabilization via computational protein design. We have introduced orbital based chemical descriptors for PCIs into the Rosetta Suite of Protein Structure Prediction Algorithms. Native-like geometries of hydrogen bonds, salt bridges, cation-pi, and pi-pi interactions are recapitulated during minimization of protein conformation. Additionally, a series of benchmarks designed to test the accuracy of the score function show that incorporation of partial covalent interaction increases discrimination of models built with the new score functions.

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