Journal of the Iranian Chemical Society

, Volume 10, Issue 5, pp 907–914 | Cite as

Unfolding mechanism of PHD2 as a vital protein: all-atom simulation approach

  • Hamid Hadi-Alijanvand
  • Ali A. Moosavi-Movahedi
  • Bahram Goliaei
Original Paper


Prolyl hydroxylase domain 2 containing protein (PHD2) is a central protein in regulation of cellular response to hypoxia. This protein controls the responses of cell to oxygen level via the regulation of hypoxia inducible factor (HIF) stability. HIF induces the expression of many genes, especially ones orchestrate angiogenesis. There are some reports that mentioned in some tumor types the level of HIF is high in spite of the presence of wild-type PHD2 and normoxic environment. Therefore, the possibility of PHD2 misfolding in some cancer cells arises. Studying such important protein unfolding pathway is insightful for possible therapeutic approaches. In this study, the unfolding pathway of PHD2 illustrates utilizing molecular dynamics simulation of protein thermal denaturation. Based on current study results, we represent the possible mechanisms of PHD2 unfolding in detail. The possible intermediates of PHD2 thermal unfolding are characterized, and the most venomous state of its unfolding pathway is introduced.


PHD2 Angiogenesis Protein unfolding pathway Molecular dynamics simulation Intermediate states Unfolding mechanism 



We gratefully acknowledge the support of the University of Tehran, Iran National Science Foundation (INSF), and the Center of Excellence in Biothermodynamics (CEBiotherm).

Supplementary material

13738_2013_227_MOESM1_ESM.tif (1.5 mb)
SI-1 To have estimation about the correspondence of PHD2 3D structure and 2D map of X, Y coordinates of PHD2 Cα along 25-ns MD, this graph is generated. Equal regions of 2D map and 3D structure are clarified via arrows. Darker regions are more populated. (TIF 1.48 mb)
13738_2013_227_MOESM2_ESM.gif (3.9 mb)
SI-2 This animated image shows the distribution of Cl+ ions in simulation space around PHD2 protein along 25-ns MD. PHD2 is represented by ribbon structure. Cl+ ions are presented via color points. Each color of point represents a specific ion with unique atom ID. As this animation demonstrates, a very small fraction of Cl+ atoms penetrated to PHD2 core. (GIF 3.91 mb)
13738_2013_227_MOESM3_ESM.gif (7 mb)
SI-3 This animated image shows the distribution of Na+ ions in simulation space around PHD2 protein along 25-ns MD. PHD2 is represented by ribbon structure. Na+ ions are presented via color points. Each color of point represents a specific ion with unique atom ID. As this animation demonstrates, substantial fraction of Na+ atoms penetrated to PHD2 core. (GIF 7.04 mb)
13738_2013_227_MOESM4_ESM.tif (679 kb)
SI-4 The APBS computed electrostatic potential (EP) of PHD2 is represented. Red surface stands for regions with negative EP. Regions with positive EP are highlighted by blue surface. (TIF 680 kb)
13738_2013_227_MOESM5_ESM.gif (3.7 mb)
SI-5 The negative electrostatic potential of PHD2 is represented via EP filed lines. This animated image shows that negative EP penetrates into PHD2 lumen, and therefore, such EP attracts positive ions to protein core. (GIF 3.73 mb)
13738_2013_227_MOESM6_ESM.tif (1.2 mb)
SI-6 This graph represents the interaction energy between ion and PHD2 residue’s types along 25-ns simulation time. Panel (a) shows interaction energies smaller than −0.5 kcal/mol. The (b) and (c) sections represent interaction energies smaller than 1.0 and 2.0 kcal/mol, respectively. The most strong attraction energies between ions and residues present in panel (c). (TIF 1.15 mb)


  1. 1.
    D.A. Tennant, R.V. Duran, H. Boulahbel, E. Gottlieb, Carcinogenesis 30, 1269–1280 (2009)CrossRefGoogle Scholar
  2. 2.
    K. Takenaga, Front Biosci. 16, 31–48 (2011)CrossRefGoogle Scholar
  3. 3.
    D. Fukumura, R.K. Jain, Microvasc. Res. 74, 72–84 (2007)CrossRefGoogle Scholar
  4. 4.
    P. Nyberg, T. Salo, R. Kalluri, Front Biosci. 13, 6537–6553 (2008)CrossRefGoogle Scholar
  5. 5.
    M. Furuya, Y. Yonemitsu, I. Aoki, Curr. Pharm. Des. 15, 1854–1867 (2009)CrossRefGoogle Scholar
  6. 6.
    D. Liao, R.S. Johnson, Cancer Metastasis Rev. 26, 281–290 (2007)CrossRefGoogle Scholar
  7. 7.
    T. Acker, K.H. Plate, Cancer Treat. Res. 117, 219–248 (2004)CrossRefGoogle Scholar
  8. 8.
    Q. Ke, M. Costa, Mol. Pharmacol. 70, 1469–1480 (2006)CrossRefGoogle Scholar
  9. 9.
    K.A. Lee, J.D. Lynd, S. O’Reilly, M. Kiupel, J.J. McCormick, J.J. LaPres, Mol. Cancer Res. 6, 829–842 (2008)CrossRefGoogle Scholar
  10. 10.
    R.J. Appelhoff, Y.M. Tian, R.R. Raval, H. Turley, A.L. Harris, C.W. Pugh, P.J. Ratcliffe, J.M. Gleadle, J. Biol. Chem. 279, 38458–38465 (2004)CrossRefGoogle Scholar
  11. 11.
    D.A. Chan, A.J. Giaccia, Br. J. Cancer 103, 1–5 (2010)CrossRefGoogle Scholar
  12. 12.
    T. Jokilehto, K. Rantanen, M. Luukkaa, P. Heikkinen, R. Grenman, H. Minn, P. Kronqvist, P.M. Jaakkola, Clin. Cancer Res. 12, 1080–1087 (2006)CrossRefGoogle Scholar
  13. 13.
    H. Zhong, A.M. De Marzo, E. Laughner, M. Lim, D.A. Hilton, D. Zagzag, P. Buechler, W.B. Isaacs, G.L. Semenza, J.W. Simons, Cancer Res. 59, 5830–5835 (1999)Google Scholar
  14. 14.
    S. Seshadri, K.A. Oberg, V.N. Uversky, Curr. Protein Pept. Sci. 10, 456–463 (2009)CrossRefGoogle Scholar
  15. 15.
    A. Sadana, T. Vo-Dinh, Biotechnol. Appl. Biochem. 33, 7–16 (2001)CrossRefGoogle Scholar
  16. 16.
    F. Ding, J.J. LaRocque, N.V. Dokholyan, J. Biol. Chem. 280, 40235–40240 (2005)CrossRefGoogle Scholar
  17. 17.
    B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S.V. Buldyrev, H.E. Stanley, N.V. Dokholyan, Biophys. J. 87, 2310–2321 (2004)CrossRefGoogle Scholar
  18. 18.
    V. Daggett, Methods Mol. Biol. 168, 215–247 (2001)Google Scholar
  19. 19.
    A. Li, V. Daggett, Proc. Natl. Acad. Sci. U S A 91, 10430–10434 (1994)CrossRefGoogle Scholar
  20. 20.
    V. Daggett, M. Levitt, J. Mol. Biol. 232, 600–619 (1993)CrossRefGoogle Scholar
  21. 21.
    M.W. van der Kamp, V. Daggett, Top. Curr. Chem. 305, 169–197 (2011)CrossRefGoogle Scholar
  22. 22.
    V. Daggett, Acc. Chem. Res. 35, 422–429 (2002)CrossRefGoogle Scholar
  23. 23.
    A.R. Fersht, V. Daggett, Cell 108, 573–582 (2002)CrossRefGoogle Scholar
  24. 24.
    R. Day, B.J. Bennion, S. Ham, V. Daggett, J. Mol. Biol. 322, 189–203 (2002)CrossRefGoogle Scholar
  25. 25.
    J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 26, 1781–1802 (2005)CrossRefGoogle Scholar
  26. 26.
    M.A. McDonough, V. Li, E. Flashman, R. Chowdhury, C. Mohr, B.M. Lienard, J. Zondlo, N.J. Oldham, I.J. Clifton, J. Lewis, L.A. McNeill, R.J. Kurzeja, K.S. Hewitson, E. Yang, S. Jordan, R.S. Syed, C.J. Schofield, Proc. Natl. Acad. Sci. USA 103, 9814–9819 (2006)CrossRefGoogle Scholar
  27. 27.
    A.D. Mackerell Jr, M. Feig, C.L. Brooks 3rd, J. Comput. Chem. 25, 1400–1415 (2004)CrossRefGoogle Scholar
  28. 28.
    W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 14(33–38), 27–38 (1996)Google Scholar
  29. 29.
    K. Lindorff-Larsen, S. Piana, R.O. Dror, D.E. Shaw, Science 334, 517–520 (2011)CrossRefGoogle Scholar
  30. 30.
    B. Zagrovic, C.D. Snow, S. Khaliq, M.R. Shirts, V.S. Pande, J. Mol. Biol. 323, 153–164 (2002)CrossRefGoogle Scholar
  31. 31.
    J.K. Myers, C.N. Pace, J.M. Scholtz, Protein Sci. 4, 2138–2148 (1995)CrossRefGoogle Scholar
  32. 32.
    R. Chowdhury, M.A. McDonough, J. Mecinovic, C. Loenarz, E. Flashman, K.S. Hewitson, C. Domene, C.J. Schofield, Structure 17, 981–989 (2009)CrossRefGoogle Scholar
  33. 33.
    S.J. Sheather, C. Jones, J. R. Stat. Soc: Ser. B (Stat. Methodol.) 53, 683–690 (1991)Google Scholar
  34. 34.
    T.F. Cox, M.A.A. Cox, Multidimensional scaling (Chapman & Hall, London, 1994)Google Scholar
  35. 35.
    N.A. Baker, D. Sept, S. Joseph, M.J. Holst, J.A. McCammon, Proc. Natl. Acad. Sci. 98, 10037–10041 (2001)CrossRefGoogle Scholar
  36. 36.
    A. Rajan, P.L. Freddolino, K. Schulten, PLoS ONE 5, e9890 (2010)CrossRefGoogle Scholar
  37. 37.
    M.S. Cheung, A.E. Garcia, J.N. Onuchic, PNAS 99, 685–690 (2002)CrossRefGoogle Scholar
  38. 38.
    Y. Levy, J.N. Onuchic, Proc. Natl. Acad. Sci. USA 101, 3325–3326 (2004)CrossRefGoogle Scholar
  39. 39.
    Y.M. Rhee, E.J. Sorin, G. Jayachandran, E. Lindahl, V.S. Pande, Proc. Natl. Acad. Sci. USA 101, 6456–6461 (2004)CrossRefGoogle Scholar

Copyright information

© Iranian Chemical Society 2013

Authors and Affiliations

  • Hamid Hadi-Alijanvand
    • 1
    • 2
  • Ali A. Moosavi-Movahedi
    • 1
    • 3
  • Bahram Goliaei
    • 1
  1. 1.Institute of Biochemistry and BiophysicsUniversity of TehranTehranIran
  2. 2.Department of Biological ScienceInstitute for Advanced Studies in Basic SciencesZanjanIran
  3. 3.Center of Excellence in Biothermodynamics, IBBUniversity of TehranTehranIran

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