Find results with:

Add another field

Search by date

to

Searching collections:

Dartmouth Dissertations

Add or remove collections

Home Dartmouth Dissertations Page 1

Reference URL

To link to the entire object, paste this link in email, IM or document

To embed the entire object, paste this HTML in website

To link to this page, paste this link in email, IM or document

To embed this page, paste this HTML in website

Experiment planning for protein structure elucidation and site-directed protein recombination.

you wish to report:

Your comment:

Your Name:

Submit

Cancel

...

Back to top

Powered by CONTENTdm®

Call No.	Ph.D. 2007
Author	Ye, Xiaoduan.
Title	Experiment planning for protein structure elucidation and site-directed protein recombination.
Date	2007
Abstract	In order to most effectively investigate protein structure and improve protein function, it is necessary to carefully plan appropriate experiments. The combinatorial number of possible experiment plans demands effective criteria and efficient algorithms to choose the one that is in some sense optimal. This thesis addresses experiment planning challenges in two significant applications. The first part of this thesis develops an integrated computational-experimental approach for rapid discrimination of predicted protein structure models by quantifying their consistency with relatively cheap and easy experiments (cross-linking and site-directed mutagenesis followed by stability measurement). In order to obtain the most information from noisy and sparse experimental data, rigorous Bayesian frameworks have been developed to analyze the information content. Efficient algorithms have been developed to choose the most informative, least expensive, and most robust experiments. The effectiveness of this approach has been demonstrated using existing experimental data as well as simulations, and it has been applied to discriminate predicted structure models of the pTfa chaperone protein from bacteriophage lambda. The second part of this thesis seeks to choose optimal breakpoint locations for protein engineering by site-directed recombination. In order to increase the possibility of obtaining folded and functional hybrids in protein recombination, it is necessary to retain the evolutionary relationships among amino acids that determine protein stability and functionality. A probabilistic hypergraph model has been developed to model these relationships, with edge weights representing their statistical significance derived from database and a protein family. The effectiveness of this model has been validated by showing its ability to distinguish functional hybrids from non-functional ones in existing experimental data. It has been proved to be NP-hard in general to choose the optimal breakpoint locations for recombination that minimize the total perturbation to these relationships, but exact and approximate algorithms have been developed for a number of important cases.
Description	xv, 184 leaves : ill. (some col.) 28 cm.
Format	application/pdf
Advisor	Chris Bailey-Kellogg
Subject	Proteins -- Structure -- Computer simulation -- Experiments. ; Amino acid sequence -- Data processing -- Experiments. Protein engineering -- Experiments. ; Recombinant proteins -- Mathematical models.
College	Dartmouth College -- Department of Computer Science.
Issuing Body	Dartmouth Dissertations are made available through the Dartmouth Digital Library.
Degree	Thesis (Ph.D.)--Dartmouth College.
Copyright	All rights reserved. No part of this book may be reproduced in any form by any electronic or mechanical means without permission in writing from the author.
DOI	http://dx.doi.org/10.1349/ddlp.1693

Find results with:

Searching collections:

Home Dartmouth Dissertations Page 1

Experiment planning for protein structure elucidation and site-directed protein recombination.

Object Description

Description

Experiment planning for protein structure elucidation and...

Experiment planning for protein structure elucidation and...

	All
	Pages Enter page numbers or page ranges separated by commas. For example: 1,3,5-12