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Structural Chemistry

, Volume 28, Issue 6, pp 1815–1822 | Cite as

The effects of single-walled carbon nanotubes (SWCNTs) on the structure and function of human serum albumin (HSA): Molecular docking and molecular dynamics simulation studies

Original Research
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Abstract

Here, the interaction of single-walled carbon nanotubes (SWCNTs) and human serum albumin (HSA) as one of the most important proteins for carrying and binding of drugs was investigated and the impact of radius to volume ratio and chirality of the SWCNTs was evaluated using molecular docking method. Molecular docking results represented that zigzag SWCNT with radius to volume ratio equal to 6.77 × 10−3 Å−2 has the most negative binding energy (−17.16 kcal mol−1) and binds to the HSA cleft by four π–cation interactions. To study the changes of HSA structure, the complex of HSA–SWCNT was subjected to 30 ns molecular dynamics simulation. The MD results showed that HSA was compressed about 2% after interaction with SWCNT. The equilibrated structure of HSA–SWCNT complex was used to compare the binding of warfarin to HSA in the absence and presence of SWCNT. The obtained results represent that warfarin-binding site was changed in the presence of SWCNT and its binding energy was increased. Really, warfarin was bound on the surface of SWCNT instead of its binding site on HSA. It means that HSA function as a carrier for warfarin is altered, the free concentration of warfarin is changed, and its release is decreased in the presence of SWCNT.

Keywords

Single-walled CNT Human serum albumin Warfarin Molecular docking Molecular dynamics simulation 

Notes

Acknowledgements

The financial support of the Research Council of University of Isfahan is gratefully acknowledged.

Supplementary material

11224_2017_963_MOESM1_ESM.docx (4.6 mb)
ESM 1 (DOCX 4691 kb)

References

  1. 1.
    Zhao YL, Nalwa HS (2006) Nanotoxicology. American Scientific Publishers, CaliforniaGoogle Scholar
  2. 2.
    Bhirde AA, Patel V, Gavard J, Zhang G, Sousa AA, Masedunskas A, Leapman RD, Weigert R, Gutkind JS, Rusling JF (2009) ACS Nano 3:307–316CrossRefGoogle Scholar
  3. 3.
    Liu N, Zhang Q, Chan-Park MB, Li C, Chen P (2009) Nanoscience in biomedicine. Springer, GermanyGoogle Scholar
  4. 4.
    Thakare VS, Das M, Jain AK, Patil S, Jain S (2010) Nanomedicine 5:1277–1301CrossRefGoogle Scholar
  5. 5.
    Gorityala B, Ma J, Wang X, Chen P, Liu X (2010) Chem Soc Rev 39:2925–2934CrossRefGoogle Scholar
  6. 6.
    Zanello LP, Zhao B, Hu H, Haddon RC (2006) Nano Lett 6:562–567CrossRefGoogle Scholar
  7. 7.
    Bhirde AA, Patel V, Gavard J (2009) ACS Nano 3:307–316CrossRefGoogle Scholar
  8. 8.
    Gilbert N (2009) Nature 460:937–937CrossRefGoogle Scholar
  9. 9.
    Donaldson K, Poland CA (2009) Nat Nanotechnol 4:708–710CrossRefGoogle Scholar
  10. 10.
    Zhao Y, Xing G, Chai Z (2008) Nat Nanotechnol 3:191–192CrossRefGoogle Scholar
  11. 11.
    Maynard AD, Aitken RJ, Butz T, Colvin V, Donaldson K, Oberdörster G, Philbert MA, Ryan J, Seaton A, Stone V, Tinkle SS, Tran L, Walker NJ, Warheit DB (2006) Nature 444:267–269CrossRefGoogle Scholar
  12. 12.
    Porter AE, Gass M, Muller K, Skepper JN, Midgley PA, Welland M (2007) Nat Nanotechnol 2:713–717CrossRefGoogle Scholar
  13. 13.
    Park KH, Chhowalla M, Iqbal Z, Sesti F (2003) J Biol Chem 278:50212–50216CrossRefGoogle Scholar
  14. 14.
    Zuo G, Huang Q, Wei G, Zhou R, Fang H (2010) ACS Nano 4:7508–7514CrossRefGoogle Scholar
  15. 15.
    Ge C, Du J, Zhao L, Wang L, Liu Y, Li D, Yang Y, Zhou R, Zhao Y, Chai Z (2011) Proc Natl Acad Sci U S A 108:16968–16973CrossRefGoogle Scholar
  16. 16.
    Shen JW, Wu T, Wang Q, Kang Y (2008) Biomaterials 29:3847–3855CrossRefGoogle Scholar
  17. 17.
    Mohammadi F, Sahihi M, Bordbar AK (2015) Spectrochim Acta A Mol Biomol Spectrosc 5:274–282CrossRefGoogle Scholar
  18. 18.
    Sahihi M, Ghayeb Y (2014) Comput Biol Med 51:44–50CrossRefGoogle Scholar
  19. 19.
    Kazemi Z, Amiri-Rudbari H, Sahihi M, Mirkhani V, Moghadam M, Tangestaninejad S, Mohammadpoor-Baltork I, Gharaghani S (2016) J Photochem Photobiol B Biol 162:448–462CrossRefGoogle Scholar
  20. 20.
    Khosravi I, Hosseini F, Khorshidifard M, Sahihi M, Amiri-Rudbari H (2016) J Mol Struct 1119:373–384CrossRefGoogle Scholar
  21. 21.
    Gong X, Li J, Lu H, Wan R, Li J, Hu J, Fang H (2007) Nat Nanotechnol 2:709–712CrossRefGoogle Scholar
  22. 22.
    Hummer G, Rasaiah JC, Noworyta JP (2001) Nature 414:188–190CrossRefGoogle Scholar
  23. 23.
    Tu Y, Xiu P, Wan R, Hu J, Zhou R, Fang H (2009) Proc Natl Acad Sci U S A 106:18120–18124CrossRefGoogle Scholar
  24. 24.
    He Z, Zhou J (2014) Carbon 78:500–509CrossRefGoogle Scholar
  25. 25.
    Giovambattista N, Lopez CF, Rossky PJ, Debenedetti PG (2008) Proc Natl Acad Sci U S A 105:2274–2279CrossRefGoogle Scholar
  26. 26.
    Cui F, Qin L, Zhang G, Liu Q, Yao X, Lei B (2008) J Pharm Biomed Anal 48:1029–1036CrossRefGoogle Scholar
  27. 27.
    Lu Y, Cui F, Fan J, Yang Y, Yao X, Li J (2009) J Lumin 129:734–740CrossRefGoogle Scholar
  28. 28.
    McCallum MM, Pawlak AJ, Shadrick WR, Simeonov A, Jadhav A, Yasgar A, Maloney DJ, Arnold LA (2014) Anal Bioanal Chem 406:1867–1875CrossRefGoogle Scholar
  29. 29.
    Li F, Feterl M, Warner JM, Day AI, Keene FR, Collins JG (2013) Dalton Trans 42:8868–8877CrossRefGoogle Scholar
  30. 30.
    Domonkos C, Zsila F, Fitos I, Visy J, Kassai R, Balint B, Kotschy A (2015) RSC Adv 5:53809–53818CrossRefGoogle Scholar
  31. 31.
    Gou Y, Zhang Y, Qi J, Zhou Z, Yang F, Liang H (2015) J Inorg Biochem 144:47–55CrossRefGoogle Scholar
  32. 32.
    Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) J Comput Chem 16:2785–2791CrossRefGoogle Scholar
  33. 33.
    Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14:33–38CrossRefGoogle Scholar
  34. 34.
    Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) J Comp Chem 19:1639–1662CrossRefGoogle Scholar
  35. 35.
    Berendsen HJC, Vander Spoel D, Van Drunen R (1995) Comput Phys Commun 91:43–56CrossRefGoogle Scholar
  36. 36.
    Lindah E, Hess B, Vander Spoel D (2001) J Mol Model 7:306–317CrossRefGoogle Scholar
  37. 37.
    Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225–11236CrossRefGoogle Scholar
  38. 38.
    Johnson ATC, Staii C, Chen M, Khamis S, Johnson R, Klein ML, Gelperin A (2006) Semiconduct Sci Technol 21:S17–S21CrossRefGoogle Scholar
  39. 39.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935CrossRefGoogle Scholar
  40. 40.
    Parrinello M, Rahman A (1981) J Appl Phys 52:7182–7190CrossRefGoogle Scholar
  41. 41.
    Berendsen HJC, Postma JPM, Van Gunsteren WF, DiNola A, Haak JR (1984) J Chem Phys 81:3684–3690CrossRefGoogle Scholar
  42. 42.
    Darden T, York D, Pedersen L (1993) J Chem Phys 98:10089–10093CrossRefGoogle Scholar
  43. 43.
    Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) J Chem Phys 103:8577–8582CrossRefGoogle Scholar
  44. 44.
    Carter DC, Ho JX (1994) Adv Protein Chem 45:153–203CrossRefGoogle Scholar
  45. 45.
    Ghuman J, Zunszain PA, Petitpas I, Bhattacharya AA, Otagiri M, Curry S (2005) J Mol Biol 353:38–52CrossRefGoogle Scholar
  46. 46.
    Sudhamalla B, Gokara M, Ahalawat N, Amooru DG, Subramanyam R (2010) J Phys Chem B 114:9054–9062CrossRefGoogle Scholar
  47. 47.
    Kiselev MA, Gryzunov IA, Dobretsov GE, Komarova MN (2001) Biofizika 46:423–427Google Scholar
  48. 48.
    Fujiwara S, Amisaki T (2006) Proteins Struct Funct Bioinf 64:730–739CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of IsfahanIsfahanIran
  2. 2.Clinical Laboratory, Health Center No. 2Isfahan University of Medical ScienceIsfahanIran

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