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Journal of Chemical Physics / Volume 135 / Issue 24 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 135, 245104 (2011); http://dx.doi.org/10.1063/1.3670877 (10 pages)

Conformational fluctuations of a protein–DNA complex and the structure and ordering of water around it

Sudipta Kumar Sinha and Sanjoy Bandyopadhyay

Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India

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(Received 13 September 2011; accepted 30 November 2011; published online 23 December 2011)

Protein–DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein–DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. SYSTEM SETUP AND SIMULATION METHODS
  3. RESULTS AND DISCUSSION
    1. Structural features of the complex
    2. Configurational entropy change on complexation
    3. Properties of water around the complex
      1. Water structure
      2. Water density profile
      3. Tetrahedral ordering and tagged potential energy of water
  4. CONCLUSIONS

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KEYWORDS and PACS

Keywords

biochemistry, DNA, molecular biophysics, molecular configurations, molecular dynamics method, proteins, water

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3670877

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    I. Andricioaei and M. Karplus, J. Chem. Phys. 115, 6289 (2001)JCPSA6000115000014006289000001.


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