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The specificity of protein-DNA inter...

Harvard University.

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The specificity of protein-DNA interactions.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	The specificity of protein-DNA interactions./
Author:	Donald, Jason Eric.
Description:	181 p.
Notes:	Adviser: Eugene I. Shakhnovich.
Contained By:	Dissertation Abstracts International68-05B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3264941
ISBN:	9780549035619

The specificity of protein-DNA interactions.
Donald, Jason Eric.

The specificity of protein-DNA interactions. - 181 p.

Adviser: Eugene I. Shakhnovich.

Thesis (Ph.D.)--Harvard University, 2007.

The study of protein-DNA specificity will continue for many years, but there are now more tools available to describe these vital interactions.

ISBN: 9780549035619Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

The specificity of protein-DNA interactions.
LDR:02923nam 2200349 a 45 001 861648
005 20100720
008 100720s2007 ||||||||||||||||| ||eng d
020 $a 9780549035619
035 $a (UMI)AAI3264941
035 $a AAI3264941
040 $a UMI $c UMI
100 1 $a Donald, Jason Eric. $3 1029366
245 1 4 $a The specificity of protein-DNA interactions.
300 $a 181 p.
500 $a Adviser: Eugene I. Shakhnovich.
500 $a Source: Dissertation Abstracts International, Volume: 68-05, Section: B, page: 3072.
502 $a Thesis (Ph.D.)--Harvard University, 2007.
520 $a The study of protein-DNA specificity will continue for many years, but there are now more tools available to describe these vital interactions.
520 $a Protein-DNA interactions are vital for living organisms. From viruses to humans, the interactions of these two different classes of biopolymers control processes as important and diverse as the expression of genes and the replication, rearrangement, and repair of DNA itself. These processes occur with exquisite specificity. It is still not well understood, however, how this specificity occurs. How does a given protein biopolymer choose one particular sequence of DNA bases over another?
520 $a The past decade has seen a great increase in the number of known protein sequences and determined structures of protein-DNA complexes. To further understand how proteins specifically target DNA, we use both of these data sources. First, using protein amino acid sequences, we study the level of sequence similarity needed to confidently predict whether two sequences have the same or different specificities for DNA. We find that the level depends on the group of proteins being studied, but that a technique motivated by percolation theory can determine the similarity level that is needed. This work also leads to the prediction of proteins that carry out unusual functions, such as very different specificities or modes of binding.
520 $a Second, we use the groupings of DNA-binding proteins to predict which amino acids have been used to make a protein specific for one DNA sequence while a related protein is specific for another DNA sequence. These predictions can guide experimental studies as well as provide starting points for design.
520 $a Finally, we consider how crystal structures can be used to describe the energetics of other protein-DNA complexes. Using methods originally developed to describe protein folding, we find the method that best uses existing structural information to determine the energetics of DNA binding.
590 $a School code: 0084.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Biophysics, General. $3 1019105
650 4 $a Chemistry, Biochemistry. $3 1017722
650 4 $a Chemistry, Physical. $3 560527
690 $a 0487
690 $a 0494
690 $a 0715
690 $a 0786
710 2 $a Harvard University. $3 528741
773 0 $t Dissertation Abstracts International $g 68-05B.
790 $a 0084
790 1 0 $a Shakhnovich, Eugene I., $e advisor
791 $a Ph.D.
792 $a 2007
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3264941