Journal of Molecular Modeling

, Volume 19, Issue 8, pp 3143–3151 | Cite as

Computational insights into the binding modes of Sr-Rex with cofactor NADH/NAD+ and operator DNA

  • Yanyan Chu
  • Weihua Li
  • Jianfeng Wang
  • Guixia Liu
  • Yun Tang
Original Paper


The transcriptional repressor Rex plays key roles in modulating respiratory gene expression. It senses the redox poise of the NAD(H) pool. Rex from Streptomyces rimosus (Sr-Rex) is a newly identified protein. Its structure and complex with substrates are not determined yet. In this study, the three-dimensional (3D) structural models of Sr-Rex dimer and its complex with cofactors were constructed by homology modeling. The stability of the constructed Sr-Rex models and the detailed interactions between Sr-Rex and cofactors were further investigated by molecular dynamics simulations. The results demonstrated that the conformation of Sr-Rex changed a lot when binding with the reduced NADH or oxidized NAD+. Once binding with NADH, the Sr-Rex dimer displayed an opener conformation, which would weaken the interaction of Sr-Rex with Rex operator DNA (ROP). Key residues responsible for the binding were then identified. The computational results were consistent with experimental results, and hence provided insights into the molecular mechanism of Sr-Rex binding with ROP and NADH/NAD+, which might be helpful for the development of biosensor.


DNA-binding protein Homology modeling Molecular dynamics NADH/NAD+ Rex 



The authors sincerely thank Prof. Meijin Guo for providing the primary sequence of Sr-Rex and helpful discussion. This work was supported by the Fundamental Research Funds for the Central Universities (Grant WY1113007) and the Shanghai Committee of Science and Technology (Grant 11DZ2260600).


  1. 1.
    Weber W, Link N, Fussenegger M (2006) A genetic redox sensor for mammalian cells. Metab Eng 8(3):273–280CrossRefGoogle Scholar
  2. 2.
    Nakamura A, Sosa A, Komori H, Kita A, Miki K (2007) Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 Å resolution. Proteins 66(3):755–759CrossRefGoogle Scholar
  3. 3.
    Brekasis D, Paget MS (2003) A novel sensor of NADH/NAD+redox poise in Streptomyces coelicolor A3(2). EMBO J 22(18):4856–4865CrossRefGoogle Scholar
  4. 4.
    Sickmier EA, Brekasis D, Paranawithana S, Bonanno JB, Paget MS, Burley SK, Kielkopf CL (2005) X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing. Structure 13(1):43–54CrossRefGoogle Scholar
  5. 5.
    McLaughlin KJ, Strain-Damerell CM, Xie K, Brekasis D, Soares AS, Paget MS, Kielkopf CL (2010) Structural basis for NADH/NAD+redox sensing by a Rex family repressor. Mol Cell 38(4):563–575CrossRefGoogle Scholar
  6. 6.
    Wang E, Bauer MC, Rogstam A, Linse S, Logan DT, von Wachenfeldt C (2008) Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex. Mol Microbiol 69(2):466–478CrossRefGoogle Scholar
  7. 7.
    Shen J, Tang ZY, Xiao CE, Guo MJ (2012) Cloning and expression of the redox-sensing transcriptional repressor Rex and in vitro DNA-binding assay of the Rex and rex operator in Streptomyces rimosus M4018. Acta Microbiologica Sinica 52(1):38–43Google Scholar
  8. 8.
    Tang ZY, Zhuang YP, Ju C, Zhang SL, Herron P, Hunter LS, Guo MJ (2011) A molecular Redox Sensor from Streptomyces rimosus M4018 for Escherichia coli. Afr J Microbiol Res 5(31):5682–5688Google Scholar
  9. 9.
  10. 10.
  11. 11.
    Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882CrossRefGoogle Scholar
  12. 12.
    Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815CrossRefGoogle Scholar
  13. 13.
    Laskowski R, Macarthur M, Moss D, Thornton J (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291CrossRefGoogle Scholar
  14. 14.
    Gribskov M (1994) Profile analysis. Methods Mol Biol 25:247–266Google Scholar
  15. 15.
    Schrödinger LLC (2008)MacroModel, version 9.6, Schrödinger, LLC, New York, NY Google Scholar
  16. 16.
    Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668–1688CrossRefGoogle Scholar
  17. 17.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935CrossRefGoogle Scholar
  18. 18.
    Li W, Tang Y, Liu H, Cheng J, Zhu W, Jiang H (2008) Probing ligand binding modes of human cytochrome P450 2 J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking. Proteins 71(2):938–949CrossRefGoogle Scholar
  19. 19.
    Zhao Y, Li W, Zeng J, Liu G, Tang Y (2008) Insights into the interactions between HIV-1 integrase and human LEDGF/p75 by molecular dynamics simulation and free energy calculation. Proteins 72(2):635–645CrossRefGoogle Scholar
  20. 20.
    Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23(3):327–341CrossRefGoogle Scholar
  21. 21.
    Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16):1999–2012CrossRefGoogle Scholar
  22. 22.
    Walker RC, de Souza MM, Mercer IP, Gould IR, Klug DR (2002) Large and fast relaxations inside a protein: calculation and measurement of reorganization energies in alcohol dehydrogenase. J Phys Chem B 106:11658–11665CrossRefGoogle Scholar
  23. 23.
    Pavelites JJ, Gao J, Bash PA, Mackerell AD (1997) A molecular mechanics force field for NAD+NADH, and the pyrophosphate groups of nucleotides. J Comput Chem 18(2):221–239CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Yanyan Chu
    • 1
  • Weihua Li
    • 1
  • Jianfeng Wang
    • 1
  • Guixia Liu
    • 1
  • Yun Tang
    • 1
  1. 1.Shanghai Key Laboratory of New Drug DesignSchool of Pharmacy, East China University of Science and TechnologyShanghaiChina

Personalised recommendations