118
Views
2
CrossRef citations to date
0
Altmetric
Research Articles

Mechanistic insights into the activity of Ptf1-p48 (pancreas transcription factor 1a): probing the interactions levels of Ptf1-p48 with E2A-E47 (transcription factor E2-alpha) and ID3 (inhibitor of DNA binding 3)

, &
Pages 1834-1852 | Received 18 Mar 2017, Accepted 24 May 2017, Published online: 15 Jun 2017

References

  • Adell, T. , Gomez-Cuadrado, A. , Skoudy, A. , Pettengill, O. S. , Longnecker, D. S. , & Real, F. X. (2000). Role of the basic helix–loop–helix transcription factor p48 in the differentiation phenotype of exocrine pancreas cancer cells. Cell Growth and Differentiation , 11 , 137–147.
  • Amadei, A. , Linssen, A. B. M. , & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins-Structure Function and Genetics , 17 , 412–425. doi:10.1002/prot.340170408
  • Artavanis-Tsakonas, S. , Rand, M. D. , & Lake, R. J. (1999). Notch signaling: Cell fate control and signal integration in development. Science , 284 , 770–776. doi:10.1126/science.284.5415.770
  • Avila, J. L. , & Kissil, J. L. (2013). Notch signaling in pancreatic cancer: Oncogene or tumor suppressor? Trends Molecular Medicine , 19 , 320–327. doi:10.1016/j.molmed.2013.03.003
  • Benezra, R. , Davis, R. L. , Lassar, A. , Tapscott, S. , Thayer, M. , Lockshon, D. , & Weintraub, H. (1990). Id: A negative regulator of helix–loop–helix DNA binding proteins. Control of terminal myogenic differentiation. The Annals of the New York Academy of Sciences , 599 , 1–11. doi:10.1111/j.1749-6632.1990.tb42359.x
  • Benezra, R. , Davis, R. L. , Lockshon, D. , Turner, D. L. , & Weintraub, H. (1990). The protein Id: A negative regulator of helix–loop–helix DNA binding proteins. Cell , 61 , 49–59. doi:10.1016/0092-8674(90)90214-Y
  • Beres, T. M. , Masui, T. , Swift, G. H. , Shi, L. , Henke, R. M. , & MacDonald, R. J. (2006). PTF1 is an organ-specific and Notch-independent basic helix–loop–helix complex containing the mammalian Suppressor of Hairless (RBP-J) or its paralogue, RBP-L. Molecular and Cellular Biology , 26 , 117–130. doi:10.1128/MCB.26.1.117-130.2006
  • Bierkamp, C. , Bonhoure, S. , Mathieu, A. , Clerc, P. , Fourmy, D. , Pradayrol, L. , & Dufresne, M. (2004). Expression of cholecystokinin-2/gastrin receptor in the murine pancreas modulates cell adhesion and cell differentiation in vivo . The American Journal of Pathology , 165 , 2135–2145. doi:10.1016/S0002-9440(10)63263-4
  • Bounpheng, M. A. , Melnikova, I. N. , Dimas, J. J. , & Christy, B. A. (1999). Identification of a novel transcriptional activity of mammalian Id proteins. Nucleic Acids Research , 27 , 1740–1746. doi:10.1093/nar/27.7.1740
  • Caliandro, R. , Rossetti, G. , & Carloni, P. (2012). Local fluctuations and conformational transitions in proteins. Journal of Chemical Theory and Computation , 8 , 4775–4785. doi:10.1021/ct300610y
  • Cockell, M. , Stolarczyk, D. , Frutiger, S. , Hughes, G. J. , Hagenbuchle, O. , & Wellauer, P. K. (1995). Binding sites for hepatocyte nuclear factor 3 beta or 3 gamma and pancreas transcription factor 1 are required for efficient expression of the gene encoding pancreatic alpha-amylase. Molecular and Cellular Biology , 15 , 1933–1941. doi:10.1128/MCB.15.4.1933
  • Colovos, C. , & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science , 2 , 1511–1519. doi:10.1002/pro.5560020916
  • De La, O. J. , Emerson, L. L. , Goodman, J. L. , Froebe, S. C. , Illum, B. E. , Curtis, A. B. , & Murtaugh, L. C. (2008). Notch and Kras reprogram pancreatic acinar cells to ductal intraepithelial neoplasia. Proceedings of the National Academy of Sciences of the USA , 105 , 18907–18912. doi:10.1073/pnas.0810111105
  • de Vries, S. J. , van Dijk, M. , & Bonvin, A. M. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols , 5 , 883–897. doi:10.1038/nprot.2010.32
  • de Vries, S. J. , van Dijk, A. D. , Krzeminski, M. , van Dijk, M. , Thureau, A. , Hsu, V. , … Bonvin, A. M. (2007). HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins , 69 , 726–733. doi:10.1002/prot.21723
  • Dufresne, M. , Clerc, P. , Dieng, M. , Edir, A. , Couvelard, A. , Delisle, M. B. , … Gigoux, V. (2011). Id3 modulates cellular localization of bHLH Ptf1-p48 protein. The International Journal of Cancer , 129 , 295–306. doi:10.1002/ijc.25668
  • Esni, F. , Ghosh, B. , Biankin, A. V. , Lin, J. W. , Albert, M. A. , Yu, X. , … Leach, S. D. (2004). Notch inhibits Ptf1 function and acinar cell differentiation in developing mouse and zebrafish pancreas. Development , 131 , 4213–4224. doi:10.1242/dev.01280
  • Ghosh, B. , & Leach, S. D. (2006). Interactions between hairy/enhancer of split-related proteins and the pancreatic transcription factor Ptf1-p48 modulate function of the PTF1 transcriptional complex. The Biochemical Journal , 393 , 679–685. doi:10.1042/BJ20051063
  • Habbe, N. , Shi, G. , Meguid, R. A. , Fendrich, V. , Esni, F. , Chen, H. , … Maitra, A. (2008). Spontaneous induction of murine pancreatic intraepithelial neoplasia (mPanIN) by acinar cell targeting of oncogenic Kras in adult mice. Proceedings of the National Academy of Sciences of the USA , 105 , 18913–18918. doi:10.1073/pnas.0810097105
  • Hess, B. (2000). Similarities between principal components of protein dynamics and random diffusion. Physical Review E , 62 , 8438–8448. doi:10.1103/PhysRevE.62.8438
  • Hess, B. , Bekker, H. , Berendsen, H. J. C. , & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry , 18 , 1463–1472. doi:10.1002/(Sici)1096-987x(199709)18:12<1463::Aid-Jcc4>3.0.Co;2-H
  • Hess, B. , Kutzner, C. , van der Spoel, D. , & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation , 4 , 435–447. doi:10.1021/ct700301q
  • Hingorani, S. R. , Petricoin, E. F. , Maitra, A. , Rajapakse, V. , King, C. , Jacobetz, M. A. , … Tuveson, D. A. (2003). Preinvasive and invasive ductal pancreatic cancer and its early detection in the mouse. Cancer Cell , 4 , 437–450. doi:10.1016/S1535-6108(03)00309-X
  • Huber, R. (1979). Conformational flexibility in protein molecules. Nature , 280 , 538–539. doi:10.1038/280538a0
  • Jemal, A. , Siegel, R. , Xu, J. , & Ward, E. (2010). Cancer statistics, 2010. CA: A Cancer Journal , 60 , 277–300. doi:10.3322/caac.20073
  • Kong, Y. , Wang, Z. , Jia, Y. , Li, P. , Hao, S. , & Wang, Y. (2016). Effects of mutants in bHLH region on structure stability and protein–DNA binding energy in DECs. Journal of Biomolecular Structure & Dynamics , 1–14. doi:10.1080/07391102.2016.1196463
  • Krapp, A. , Knofler, M. , Frutiger, S. , Hughes, G. J. , Hagenbuchle, O. , & Wellauer, P. K. (1996). The p48 DNA-binding subunit of transcription factor PTF1 is a new exocrine pancreas-specific basic helix–loop–helix protein. The EMBO Journal , 15 , 4317–4329.
  • Krissinel, E. (2010). Crystal contacts as nature’s docking solutions. Journal of Computational Chemistry , 31 , 133–143. doi:10.1002/jcc.21303
  • Kruger, D. M. , & Gohlke, H. (2010). DrugScorePPI webserver: Fast and accurate in silico alanine scanning for scoring protein–protein interactions. Nucleic Acids Research , 38 , W480–486. doi:10.1093/nar/gkq471
  • Laskowski, R. A. , Macarthur, M. W. , Moss, D. S. , & Thornton, J. M. (1993). Procheck – A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography , 26 , 283–291. doi:10.1107/S0021889892009944
  • Lin, J. H. (2011). Accommodating protein flexibility for structure-based drug design. Current Topics in Medicinal Chemistry , 11 , 171–178. doi:10.2174/156802611794863580
  • Lindorff-Larsen, K. , Piana, S. , Palmo, K. , Maragakis, P. , Klepeis, J. L. , Dror, R. O. , & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins , 78 , 1950–1958. doi:10.1002/prot.22711
  • Maia, A. M. , da Silva, J. H. , Mencalha, A. L. , Caffarena, E. R. , & Abdelhay, E. (2012). Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants. BMC Bioinformatics , 13 , 184. doi:10.1186/1471-2105-13-184
  • Maisuradze, G. G. , & Leitner, D. M. (2007). Free energy landscape of a biomolecule in dihedral principal component space: Sampling convergence and correspondence between structures and minima. Proteins , 67 , 569–578. doi:10.1002/prot.21344
  • Martonak, R. , Laio, A. , & Parrinello, M. (2003). Predicting crystal structures: The Parrinello–Rahman method revisited. Physical Review Letters , 90 , 075503. doi:10.1103/PhysRevLett. 90.075503
  • Miyamoto, S. , & Kollman, P. A. (1992). Settle – An analytical version of the shake and rattle algorithm for rigid water models. Journal of Computational Chemistry , 13 , 952–962. doi:10.1002/jcc.540130805
  • Miyamoto, Y. , Maitra, A. , Ghosh, B. , Zechner, U. , Argani, P. , Iacobuzio-Donahue, C. A. , & Leach, S. D. (2003). Notch mediates TGF alpha-induced changes in epithelial differentiation during pancreatic tumorigenesis. Cancer Cell , 3 , 565–576. doi:10.1016/S1535-6108(03)00140-5
  • Molero, X. , Adell, T. , Skoudy, A. , Padilla, M. A. , Gomez, J. A. , Chalaux, E. , … Real, F. X. (2007). Pancreas transcription factor 1alpha expression is regulated in pancreatitis. European Journal of Clinical Investigation , 37 , 791–801. doi:10.1111/j.1365-2362.2007.01856.x
  • Muthu, K. , Panneerselvam, M. , Jayaraman, M. , Topno, N. S. , Das, A. A. , & Ramadas, K. (2012). Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: Molecular docking and dynamics studies. Journal of Molecular Modeling , 18 , 4865–4884. doi:10.1007/s00894-012-1489-x
  • Muthu, K. , Panneerselvam, M. , Topno, N. S. , Jayaraman, M. , & Ramadas, K. (2015). Structural perspective of ARHI mediated inhibition of STAT3 signaling: An insight into the inactive to active transition of ARHI and its interaction with STAT3 and importinbeta. Cellular Signalling , 27 , 739–755. doi:10.1016/j.cellsig.2014.11.036
  • Muthu, K. , Panneerselvam, M. , Topno, N. S. , & Ramadas, K. (2016). Structural transition of ETS1 from an auto-inhibited to functional state upon association with the p16 INK4a native and mutated promoter region. RSC Advances , 6 , 15960–15975. doi:10.1039/C5RA24525G
  • Nocker, M. , & Cozzini, P. (2011). Induced fit simulations on nuclear receptors. Current Topics in Medicinal Chemistry , 11 , 133–147. doi:10.2174/156802611794863526
  • Norton, J. D. (2000). ID helix–loop–helix proteins in cell growth, differentiation and tumorigenesis. The Journal of Cell Science , 113 , 3897–3905.
  • Pesce, S. , & Benezra, R. (1993). The loop region of the helix–loop–helix protein Id1 is critical for its dominant negative activity. Molecular and Cellular Biology , 13 , 7874–7880. doi:10.1128/MCB.13.12.7874
  • Roux, E. , Strubin, M. , Hagenbuchle, O. , & Wellauer, P. K. (1989). The cell-specific transcription factor PTF1 contains two different subunits that interact with the DNA. Genes & Development , 3 , 1613–1624. doi:10.1101/gad.3.10.1613
  • Roy, A. , Kucukural, A. , & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols , 5 , 725–738. doi:10.1038/nprot.2010.5
  • Shuno, Y. , Tsuno, N. H. , Okaji, Y. , Tsuchiya, T. , Sakurai, D. , Nishikawa, T. , … Nagawa, H. (2010). Id1/Id3 knockdown inhibits metastatic potential of pancreatic cancer. The Journal of Surgical Research , 161 , 76–82. doi:10.1016/j.jss.2008.10.031
  • Sommer, L. , Hagenbuchle, O. , Wellauer, P. K. , & Strubin, M. (1991). Nuclear targeting of the transcription factor PTF1 is mediated by a protein subunit that does not bind to the PTF1 cognate sequence. Cell , 67 , 987–994. doi:10.1016/0092-8674(91)90371-5
  • Teilum, K. , Olsen, J. G. , & Kragelund, B. B. (2011). Protein stability, flexibility and function. Biochimica et Biophysica Acta , 1814 , 969–976. doi:10.1016/j.bbapap.2010.11.005
  • Topno, N. S. , Kannan, M. , & Krishna, R. (2016). Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor – An Insight through molecular dynamics and docking approach. Biochemistry and Biophysics Reports , 5 , 180–190. doi:10.1016/j.bbrep.2015.12.002
  • Van Der Spoel, D. , Lindahl, E. , Hess, B. , Groenhof, G. , Mark, A. E. , & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry , 26 , 1701–1718. doi:10.1002/jcc.20291
  • Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics , 9 , 40. doi:10.1186/1471-2105-9-40

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.