Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/34481
Title: Interaction of EcoRI with Noncognate DNA Sequences: Computational Investigation of Dynamics of Protein & Water and DNA Conformation
Authors: VIGNESHWAR RAMAKRISHNAN
Keywords: EcoRI, Intrinsic Protein Dynamics, Water Dynamics, DNA Conformation, Molecular Dynamics Simulations, Protein-DNA interaction
Issue Date: 4-Jan-2012
Source: VIGNESHWAR RAMAKRISHNAN (2012-01-04). Interaction of EcoRI with Noncognate DNA Sequences: Computational Investigation of Dynamics of Protein & Water and DNA Conformation. ScholarBank@NUS Repository.
Abstract: Protein-DNA interactions form the basis for many cellular processes. How a protein rapidly identifies its target (cognate) DNA sequence from among a sea of random (noncognate) sequences is an intriguing area. In this thesis, changes in the protein dynamics, water dynamics and sequence-dependent changes in DNA conformation when EcoRI binds to a noncognate sequence that differs from the cognate sequence by a single basepair was investigated using molecular dynamics simulations. The results suggest that when EcoRI chances upon its cognate sequence, specific domains in the protein undergo dynamical changes, which, along with the reduction in the dynamics of water in the hydration layer and sequence-dependent DNA conformational changes promote the formation of a stable complex. Even a minimal mutation of the DNA sequence is enough to alter the DNA conformation, the dynamics of the interfacial residues and the dynamics of water making the complex unfit for required function.
URI: http://scholarbank.nus.edu.sg/handle/10635/34481
Appears in Collections:Ph.D Theses (Open)

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