A Caltech Library Service

Exploration of the Determinants of Protein Structure and Stability by Protein Design


Sarisky, Catherine Ann (2005) Exploration of the Determinants of Protein Structure and Stability by Protein Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/RBSA-R089.


Optimization of Rotamers by Iterative Techniques (ORBIT) has been used to calculate novel sequences for several small proteins. A partial sequence design (20 of 28 residues) is described for the zinc finger Zif268 (beta-beta-alpha) motif. The designed peptide folds without a metal cofactor, despite its small size and the avoidance of the disulfides and unnatural amino acids that are often used to stabilize peptide structures. The utility of ORBIT for predicting the relative stabilities of a series of beta-beta-alpha peptides was investigated. A good correlation between theoretical and experimental stabilities was observed except when the turn residues were changed. This observation led to the discovery that some of these peptides had an unexpected turn conformation. This information was used to design a peptide that is more stable than the original peptide sequence produced with ORBIT.

The tolerance of ORBIT for altered backbone coordinates was investigated using the protein domain G-beta1. It was determined that altering the coordinates of the backbone template used in ORBIT altered the sequences selected, but that the fold did not change as a result. The G-beta1 domain was also used to parameterize a methionine inclusion penalty, allowing the inclusion of methionine in ORBIT design calculations while preventing indiscriminate inclusion of methionine at sites where a less flexible side-chain will fit.

Lastly, some preliminary work on using ORBIT to design DNA binding interfaces is discussed.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:dead end elimination; gb1; protein design; protein structure
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Mayo, Stephen L.
Thesis Committee:
  • Roberts, Richard W. (chair)
  • Rees, Douglas C.
  • Dervan, Peter B.
  • Mayo, Stephen L.
Defense Date:27 April 2005
Non-Caltech Author Email:sarisky (AT)
Record Number:CaltechETD:etd-05272005-121337
Persistent URL:
Sarisky, Catherine Ann0000-0002-7692-2517
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:2148
Deposited By: Imported from ETD-db
Deposited On:27 May 2005
Last Modified:23 Jul 2020 21:38

Thesis Files

PDF (sarisky_phd.pdf) - Final Version
See Usage Policy.


Repository Staff Only: item control page