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.
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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
Blessia TF, Sharmila DJS, Samian MR, Arsad H, Jamil NF (2012) Int Res J Pharm I(3):251–256
Darie CC (2013) Aust J Chem 66:1–2
Darie CC, Litscher ES, Wassarman PM (2008) Structure, processing, and polymerization of rainbow trout egg vitelline envelope proteins. Springer-Verlag, Düsseldorf
De Rosa MC, Pirolli D, Bozzi M, Sciandra F, Giardina B, Brancaccio A (2011) J Mol Graph Model 29:1015–1024
Dodson G, Verma CS (2006) Cell Mol Life Sci 63:207–219
Hinsen K, Kneller GR (2008) Proteins 70:1235–1242
Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14:33–38
Hussain MR, Shaik NA, Al-Aama JY, Asfour HZ, Khan FS, Masoodi TA, Khan MA, Shaik NS (2012) Gene 508:188–196
Iavarone AT, Patriksson A, Van der Spoel D, Parks JH (2007) J Am Chem Soc 129:6726–6735
Karplus M, Kuriyan J (2005) Proc Natl Acad Sci USA 102:6679–6685
Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS (2011) J Bacteriol 193:6517–6528
Khairudin NBA, Wahab HA (2012) Int J Mod Phys Conf Ser 9:193–198
Mao Y, Woenckhaus J, Kolafa J, Ratner MA, Jarrold MF (1999) J Am Chem Soc 121:2712–2721
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
Nordling E, Abraham-Nordling M (2012) Comput Biol Chem 39:29–34
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) J Comput Chem 25:1605–1612
Platica M, Chen HZ, Ciurea D, Gil J, Mandeli J, Hollander VP (1992) Endocrinology 131:2573–2580
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
Rizzuti B, Daggett V (2013) Arch Biochem Biophys 531:128–135
Rosas-Trigueros JL, Ilizaliturri-Flores I, Benitez-Cardoza CG, Correa-Basurto J, Zamorano-Carrillo A (2012) Curr Med Chem 19:6081–6094
Rossky PJ, Karplus M (1979) J Am Chem Soc 101:1913–1937
Roy A, Kucukural A, Zhang Y (2010) Nat Protoc 5:725–738
Roy U, Sokolowska I, Woods AG, Darie CC (2012) Biotechnol Appl Biochem 59:445–450
Shaikh SA, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E (2013) Biochemistry 52:569–587
Shi W, Inamdar MV, Sastry AM, Lastoskie CM (2007) J Phys Chem C 111:15642–15652
Software: Accelrys Software Inc. (2012) Discovery studio modeling environment, Release 3.5. Accelrys Software Inc., San Diego
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
Sokolowska I, Woods AG, Gawinowicz MA, Roy U, Darie CC (2012) FEBS J 279:2579–2594
Sokolowska I, Woods AG, Gawinowicz MA, Roy U, Darie CC (2012) J Biol Chem 287:1719–1733
Thirumuruganandham SP, Urbassek HM (2010) Bioche Res Int 2010:6
Van Gunsteren WF, Karplus M (1982) Biochemistry 21:2259–2274
Woods AG, Sokolowska I, Deinhardt K, Sandu C, Darie CC (2013) Brain Struct Funct. doi:10.1007/s00429-013-0571-1
Zhang Y (2008) BMC Bioinformatics 9:40
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.
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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
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DOI: https://doi.org/10.1007/s10930-013-9510-5