Deformation Energy Analysis of Base Step Substitution in Protein-DNA Interactions
Date Issued
2009
Date
2009
Author(s)
Yang, Chun-Shu
Abstract
Studies of recognition between DNA and protein most focus on the direct contacts. In fact, amino acids recognize specific DNA sequences not only through direct contacts but also utilizing indirect interaction. Many studies have shown that mutations of base that are not in contact with any amino acids also affect binding affinities. Examples of indirect affection are proteins may recognize a DNA sequence via water-mediated contacts, sequence-dependent conformational features, or binding-induced distortion of the DNA. The purpose of this thesis is to analyze the DNA structure of protein-DNA complexes collected in Protein Data Bank. After calculation of DNA conformational parameters, base steps are clustered based on parameters and base steps with similar conformations are analyzed from the aspect of binding free energy. Statistical analysis concludes that some substitution of similar base step pairs can be the prior consideration when randomizing DNA sequences.
Subjects
base pair step
deformation energy
clustering
DNA variability
Type
thesis
File(s)![Thumbnail Image]()
Loading...
Name
ntu-98-R96631030-1.pdf
Size
23.32 KB
Format
Adobe PDF
Checksum
(MD5):84cb94cf325dd882a0a75e00b89a6294