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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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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 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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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