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Int. J. Mol. Sci. 2012, 13(6), 7138-7148; doi:10.3390/ijms13067138

Target Molecular Simulations of RecA Family Protein Filaments

1
Department of Information Management, Chia Nan University of Pharmacy & Science, No. 60, Sec. 1, Erren Rd., Rende Dist., Tainan City 71710, Taiwan
2
National Center for High-Performance Computing, Hsin-Shi, No. 28, Nan-Ke 3rd Rd., Hsin-Shi Dist., Tainan City 74147, Taiwan
3
Department of Physics, National Chung Hsing University, No. 250, Kuo Kuang Rd., Taichung 402, Taiwan
*
Author to whom correspondence should be addressed.
Received: 11 April 2012 / Revised: 10 May 2012 / Accepted: 29 May 2012 / Published: 11 June 2012
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Abstract

Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon. We find 11 rotary residues (R72, T75-K81, M84, V86 and K87) and five zero rotary residues (I71, K74, E82, R83 and K88) in the simulations. Inclusion of our simulations may help to understand the RadA family mechanism.
Keywords: molecular dynamics; homology modeling; archaeal rada; DNA SOS repair process; ATP binding proteins molecular dynamics; homology modeling; archaeal rada; DNA SOS repair process; ATP binding proteins
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Su, Z.-Y.; Lee, W.-J.; Su, W.-S.; Wang, Y.-T. Target Molecular Simulations of RecA Family Protein Filaments. Int. J. Mol. Sci. 2012, 13, 7138-7148.

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