Skip to main content
Log in

Structural Evaluation and Analyses of Tumor Differentiation Factor

  • Published:
The Protein Journal Aims and scope Submit manuscript

Abstract

Tumor differentiation factor (TDF) is a protein produced by the pituitary and secreted into the blood stream. The mechanism of its action has still not been elucidated, although the associated protein receptor was identified. Furthermore, the TDF protein does not have any homology with other known proteins, and the crystal structure of TDF also is not available at this time. To gain some insight into the structure of this rather underexplored protein, we have performed a molecular dynamics simulation of a model TDF structure. The structural stability of this protein is evaluated as a function of time. The time dependent structural changes of four cysteine residues present in this structure also are explored.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Abbreviations

MD:

Molecular dynamics

TDF:

Tumor differentiation factor

rTDF:

Recombinant TDF

Cys:

Cysteine

Ps:

Picosecond

RMSD:

Root mean square deviation

RMSF:

Root mean square fluctuation

SASA:

Solvent accessible surface area

References

  1. Blessia TF, Sharmila DJS, Samian MR, Arsad H, Jamil NF (2012) Int Res J Pharm I(3):251–256

    Google Scholar 

  2. Darie CC (2013) Aust J Chem 66:1–2

    Article  Google Scholar 

  3. Darie CC, Litscher ES, Wassarman PM (2008) Structure, processing, and polymerization of rainbow trout egg vitelline envelope proteins. Springer-Verlag, Düsseldorf

    Book  Google Scholar 

  4. De Rosa MC, Pirolli D, Bozzi M, Sciandra F, Giardina B, Brancaccio A (2011) J Mol Graph Model 29:1015–1024

    Article  Google Scholar 

  5. Dodson G, Verma CS (2006) Cell Mol Life Sci 63:207–219

    Article  CAS  Google Scholar 

  6. Hinsen K, Kneller GR (2008) Proteins 70:1235–1242

    Article  CAS  Google Scholar 

  7. Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14:33–38

    Article  CAS  Google Scholar 

  8. Hussain MR, Shaik NA, Al-Aama JY, Asfour HZ, Khan FS, Masoodi TA, Khan MA, Shaik NS (2012) Gene 508:188–196

    Article  CAS  Google Scholar 

  9. Iavarone AT, Patriksson A, Van der Spoel D, Parks JH (2007) J Am Chem Soc 129:6726–6735

    Article  CAS  Google Scholar 

  10. Karplus M, Kuriyan J (2005) Proc Natl Acad Sci USA 102:6679–6685

    Article  CAS  Google Scholar 

  11. Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS (2011) J Bacteriol 193:6517–6528

    Article  CAS  Google Scholar 

  12. Khairudin NBA, Wahab HA (2012) Int J Mod Phys Conf Ser 9:193–198

    Article  CAS  Google Scholar 

  13. Mao Y, Woenckhaus J, Kolafa J, Ratner MA, Jarrold MF (1999) J Am Chem Soc 121:2712–2721

    Article  CAS  Google Scholar 

  14. Ngounou Wetie AG, Sokolowska I, Wormwood K, Michel TM, Thome J, Darie CC, Woods AG et al (2013) J Mol Psychiatry 1:8. doi:10.1186/2049-9256-1-8

  15. Nordling E, Abraham-Nordling M (2012) Comput Biol Chem 39:29–34

    Article  CAS  Google Scholar 

  16. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) J Comput Chem 25:1605–1612

    Article  CAS  Google Scholar 

  17. Platica M, Chen HZ, Ciurea D, Gil J, Mandeli J, Hollander VP (1992) Endocrinology 131:2573–2580

    CAS  Google Scholar 

  18. Platica M, Ivan E, Holland JF, Ionescu A, Chen S, Mandeli J, Unger PD, Platica O (2004) Proc Natl Acad Sci USA 101:1560–1565

    Article  CAS  Google Scholar 

  19. Rizzuti B, Daggett V (2013) Arch Biochem Biophys 531:128–135

    Article  CAS  Google Scholar 

  20. Rosas-Trigueros JL, Ilizaliturri-Flores I, Benitez-Cardoza CG, Correa-Basurto J, Zamorano-Carrillo A (2012) Curr Med Chem 19:6081–6094

    Article  CAS  Google Scholar 

  21. Rossky PJ, Karplus M (1979) J Am Chem Soc 101:1913–1937

    Article  CAS  Google Scholar 

  22. Roy A, Kucukural A, Zhang Y (2010) Nat Protoc 5:725–738

    Article  CAS  Google Scholar 

  23. Roy U, Sokolowska I, Woods AG, Darie CC (2012) Biotechnol Appl Biochem 59:445–450

    Article  CAS  Google Scholar 

  24. Shaikh SA, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E (2013) Biochemistry 52:569–587

    Article  CAS  Google Scholar 

  25. Shi W, Inamdar MV, Sastry AM, Lastoskie CM (2007) J Phys Chem C 111:15642–15652

    Article  CAS  Google Scholar 

  26. Software: Accelrys Software Inc. (2012) Discovery studio modeling environment, Release 3.5. Accelrys Software Inc., San Diego

  27. Sokolowska I, Woods AG, Gawinowicz MA, Roy U, Darie CC (2013) Cell Mol Life Sci 70(16):2835–2848. doi:10.1007/s00018-012-1185-0

    Google Scholar 

  28. Sokolowska I, Woods AG, Gawinowicz MA, Roy U, Darie CC (2012) FEBS J 279:2579–2594

    Article  CAS  Google Scholar 

  29. Sokolowska I, Woods AG, Gawinowicz MA, Roy U, Darie CC (2012) J Biol Chem 287:1719–1733

    Article  CAS  Google Scholar 

  30. Thirumuruganandham SP, Urbassek HM (2010) Bioche Res Int 2010:6

    Google Scholar 

  31. Van Gunsteren WF, Karplus M (1982) Biochemistry 21:2259–2274

    Article  Google Scholar 

  32. Woods AG, Sokolowska I, Deinhardt K, Sandu C, Darie CC (2013) Brain Struct Funct. doi:10.1007/s00429-013-0571-1

  33. Zhang Y (2008) BMC Bioinformatics 9:40

    Article  Google Scholar 

Download references

Acknowledgments

We are thankful to Professor John B. McLaughlin for allowing us access to the Materials Studio software. This work was supported in part by the Keep A Breast Foundation (KEABF-375-35054) and by support from the U.S. Army research office through the Defense University Research Instrumentation Program (DURIP Grant #W911NF-11-1-0304). This work was also supported in part by Mary Joyce, Kenneth Sandler, Robert Matloff, and by the SciFund challenge contributors. CCD was supported during the summer of 2013 by the David A. Walsh’67 fellowship.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Costel C. Darie.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Roy, U., Woods, A.G., Sokolowska, I. et al. Structural Evaluation and Analyses of Tumor Differentiation Factor. Protein J 32, 512–518 (2013). https://doi.org/10.1007/s10930-013-9510-5

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10930-013-9510-5

Keywords

Navigation