The D83V mutation in the myocyte-specific enhancer factor-2 beta (MEF2B) gene is frequently observed in lymphomas. Surprisingly, this apparent gain-of-function mutation is within a protein that is involved in the promotion of apoptosis in B cells. To investigate the oncogenic effects of this alteration and explain its predominance over other known loss-of-function mutations of MEF2B, we propose a hypothesis that this mutation influences the dynamic folding of the C-terminal loop of the N-terminal domain of MEF2B. According to our hypothesis, the mutation allows MEF2B to bind promiscuously to a wider variety of gene promoters. A large set of molecular dynamic simulations (MD) was conducted to investigate the effects of D83V mutation in silico and support the hypothesis. 1. Introduction The myocyte-specific enhancer factor-2 (MEF2) family of transcription factors plays an essential role in myogenesis [1, 2] and the regulation of the proapoptotic gene Nur77 [3–6]. This family is composed of four members, MEF2A, -B, -C, and -D, which normally function either as homo- or heterodimers [7]. All of these factors recognize the DNA consensus sequence C/TTA(A/T)4TAG/A, which is present within many gene promoters (see [8, 9] and references therein), and consist of a MADS-box containing a N-terminal domain responsible for DNA recognition and dimerization and an as yet uncharacterized C-terminal domain [10]. The sequence differences between the N-terminal domain of MEF2 forms are mainly within the MEF2S subdomain (residues 58–95) of the N-terminal domain which is responsible for the determining of DNA binding specificity [11–18]. Recently, MEF2B was found to be altered in many B-cell-derived lymphomas [19]. Morin et al. [19] and Youn and Liu [20] proposed a model of MEF2B involvement in the development of lymphomas through dependent signaling downstream of the B-cell receptor. In normal germinal centre B-cells MEF2B binds to the promoter of Nur77, a proapoptotic gene that plays a crucial role in TCR-mediated apoptosis [21–23]. However, MEF2B is kept transcriptionally inactive by the suppressor Cabin1 which binds to its N-terminal domain preventing the transcription of Nur77. This repression is calcium-dependent [3, 4]: when enters the cytoplasm in response to B-cell receptor activation, it folds the intrinsically unstructured Calmodulin, which becomes a more preferred partner of Cabin1. Calmodulin in complex with releases Cabin1 from its complex with MEF2B, allowing MEF2B to initiate Nur77 transcription and recruit other activating factors such as HDAC7, HDAC9, and
References
[1]
L. A. Gossett, D. J. Kelvin, E. A. Sternberg, and E. N. Olson, “A new myocyte-specific enhancer-binding factor that recognizes a conserved element associated with multiple muscle-specific genes,” Molecular and Cellular Biology, vol. 9, no. 11, pp. 5022–5033, 1989.
[2]
B. L. Black and E. N. Olson, “Transcriptional control of muscle development by myocyte enhancer factor-2 (MEF2) proteins,” Annual Review of Cell and Developmental Biology, vol. 14, pp. 167–196, 1998.
[3]
J. D. Woronicz, B. Calnan, V. Ngo, and A. Winoto, “Requirement for the orphan steroid receptor Nur77 in apoptosis of T-cell hybridomas,” Nature, vol. 367, no. 6460, pp. 277–281, 1994.
[4]
J. D. Woronicz, A. Lina, B. J. Calnan, S. Szychowski, L. Cheng, and A. Winoto, “Regulation of the Nur77 orphan steroid receptor in activation-induced apoptosis,” Molecular and Cellular Biology, vol. 15, no. 11, pp. 6364–6376, 1995.
[5]
H.-D. Youn, L. Sun, R. Prywes, and J. O. Liu, “Apoptosis of T cells mediated by Ca2+-induced release of the transcription factor MEF2,” Science, vol. 286, no. 5440, pp. 790–793, 1999.
[6]
H.-D. Youn, T. A. Chatila, and J. O. Liu, “Integration of calcineurin and MEF2 signals by the coactivator p300 during T-cell apoptosis,” EMBO Journal, vol. 19, no. 16, pp. 4323–4331, 2000.
[7]
J. F. Martin, J. M. Miano, C. M. Hustad, N. G. Copeland, N. A. Jenkins, and E. N. Olson, “A Mef2 gene that generates a muscle-specific isoform via alternative mRNA splicing,” Molecular and Cellular Biology, vol. 14, no. 3, pp. 1647–1656, 1994.
[8]
J. D. Molkentin, B. L. Black, J. F. Martin, and E. N. Olson, “Mutational analysis of the DNA binding, dimerization, and transcriptional activation domains of MEF2C,” Molecular and Cellular Biology, vol. 16, no. 6, pp. 2627–2636, 1996.
[9]
V. Andres, M. Cervera, and V. Mahdavi, “Determination of the consensus binding site for MEF2 expressed in muscle and brain reveals tissue-specific sequence constraints,” Journal of Biological Chemistry, vol. 270, no. 40, pp. 23246–23249, 1995.
[10]
K. Huang, J. M. Louis, L. Donaldson, F.-L. Lim, A. D. Sharrocks, and G. M. Clore, “Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors,” EMBO Journal, vol. 19, no. 11, pp. 2615–2628, 2000.
[11]
E. Dodou, D. B. Sparrow, T. Mohun, and R. Treisman, “MEF2 proteins, including MEF2A, are expressed in both muscle and non-muscle cells,” Nucleic Acids Research, vol. 23, no. 21, pp. 4267–4274, 1995.
[12]
D. Meierhans, M. Sieber, and R. K. Allemann, “High affinity binding of MEF-2C correlates with DNA bending,” Nucleic Acids Research, vol. 25, no. 22, pp. 4537–4544, 1997.
[13]
D. Meierhans and R. K. Allemann, “The N-terminal methionine is a major determinant of the DNA binding specificity of MEF-2C,” Journal of Biological Chemistry, vol. 273, no. 40, pp. 26052–26060, 1998.
[14]
S. J. Nurrish and R. Treisman, “DNA binding specificity determinants in MADS-box transcription factors,” Molecular and Cellular Biology, vol. 15, no. 8, pp. 4076–4085, 1995.
[15]
R. Pollock and R. Treisman, “Human SRF-related proteins: DNA-binding properties and potential regulatory targets,” Genes and Development, vol. 5, no. 12, pp. 2327–2341, 1991.
[16]
A. D. Sharrocks, F. Von Hesler, and P. E. Shaw, “The identification of elements determining the different DNA binding specificities of the MADS box proteins p67(SRF) and RSRFC4,” Nucleic Acids Research, vol. 21, no. 2, pp. 215–221, 1993.
[17]
A. G. West and A. D. Sharrocks, “MADS-box transcription factors adopt alternative mechanisms for bending DNA,” Journal of Molecular Biology, vol. 286, no. 5, pp. 1311–1323, 1999.
[18]
A. G. West, B. E. Causier, B. Davies, and A. D. Sharrocks, “DNA binding and dimerisation determinants of antirrhinum majus MADS-box transcription factors,” Nucleic Acids Research, vol. 26, no. 23, pp. 5277–5287, 1998.
[19]
R. D. Morin, M. Mendez-Lago, A. J. Mungall et al., “Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma,” Nature, vol. 476, no. 7360, pp. 298–303, 2011.
[20]
H.-D. Youn and J. O. Liu, “Cabin1 represses MEF2-dependent Nur77 expression and T cell apoptosis by controlling association of histone deacetylases and acetylases with MEF2,” Immunity, vol. 13, no. 1, pp. 85–94, 2000.
[21]
A. Winoto, “Cell death in the regulation of immune responses,” Current Opinion in Immunology, vol. 9, no. 3, pp. 365–370, 1997.
[22]
B. Wong and Y. Choi, “Pathways leading to cell death in T cells,” Current Opinion in Immunology, vol. 9, no. 3, pp. 358–364, 1997.
[23]
E. Sebzda, S. Mariathasan, T. Ohteki, R. Jones, M. F. Bachmann, and P. S. Ohashi, “Selection of the T cell repertoire,” Annual Review of Immunology, vol. 17, pp. 829–874, 1999.
[24]
L. Sun, H.-D. Youn, C. Loh, M. Stolow, W. He, and J. O. Liu, “Cabin 1, a negative regulator for calcineurin signaling in T lymphocytes,” Immunity, vol. 8, no. 6, pp. 703–711, 1998.
[25]
O. I. Ornatsky, D. M. Cox, P. Tangirala et al., “Post-translational control of the MEF2A transcriptional regulatory protein,” Nucleic Acids Research, vol. 27, no. 13, pp. 2646–2654, 1999.
[26]
R. L. S. Perry, C. Yang, N. Soora et al., “Direct interaction between Myocyte Enhancer Factor 2 (MEF2) and protein phosphatase 1α represses MEF2-dependent gene expression,” Molecular and Cellular Biology, vol. 29, no. 12, pp. 3355–3366, 2009.
[27]
J. D. Molkentin, B. L. Black, J. F. Martin, and E. N. Olson, “Cooperative activation of muscle gene expression by MEF2 and myogenic bHLH proteins,” Cell, vol. 83, no. 7, pp. 1125–1136, 1995.
[28]
E. Santelli and T. J. Richmond, “Crystal structure of MEF2A core bound to DNA at 1.5 ？ resolution,” Journal of Molecular Biology, vol. 297, no. 2, pp. 437–449, 2000.
[29]
J. He, J. Ye, Y. Cai et al., “Structure of p300 bound to MEF2 on DNA reveals a mechanism of enhanceosome assembly,” Nucleic Acids Research, vol. 39, no. 10, pp. 4464–4474, 2011.
[30]
A. Han, J. He, Y. Wu, J. O. Liu, and L. Chen, “Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2,” Journal of Molecular Biology, vol. 345, no. 1, pp. 91–102, 2005.
[31]
A. Han, F. Pan, J. C. Stroud, H.-D. Youn, J. O. Liu, and L. Chen, “Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2,” Nature, vol. 422, no. 6933, pp. 730–734, 2003.
[32]
Y. Wu, R. Dey, A. Han et al., “Structure of the MADS-box/MEF2 Domain of MEF2A Bound to DNA and its implication for myocardin recruitment,” Journal of Molecular Biology, vol. 397, no. 2, pp. 520–533, 2010.
[33]
G. N. Patey and J. P. Valleau, “The free energy of spheres with dipoles: Monte Carlo with multistage sampling,” Chemical Physics Letters, vol. 21, no. 2, pp. 297–300, 1973.
[34]
C. H. Bennett, “Efficient estimation of free energy differences from Monte Carlo data,” Journal of Computational Physics, vol. 22, no. 2, pp. 245–268, 1976.
[35]
D. Wu and D. A. Kofke, “Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation,” The Journal of Chemical Physics, vol. 123, no. 5, Article ID 054103, 2005.
[36]
J. A. Lemkul and D. R. Bevan, “Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics,” Journal of Physical Chemistry B, vol. 114, no. 4, pp. 1652–1660, 2010.
[37]
K. Murata, Y. Sugita, and Y. Okamoto, “Free energy calculations for DNA base stacking by replica-exchange umbrella sampling,” Chemical Physics Letters, vol. 385, no. 1-2, pp. 1–7, 2004.
[38]
N. Huang, N. K. Banavali, and A. D. MacKerell Jr., “Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 1, pp. 68–73, 2003.
[39]
T. W. Allen, T. Ba？tu？, S. Kuyucak, and S.-H. Chung, “Gramicidin A channel as a test ground for molecular dynamics force fields,” Biophysical Journal, vol. 84, no. 4, pp. 2159–2168, 2003.
[40]
L. Dai, Y. Mu, L. Nordenski？ld, and J. R. C. van der Maarel, “Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules,” Physical Review Letters, vol. 100, no. 11, Article ID 118301, 2008.
[41]
W. F. D. Bennett, J. L. MacCallum, M. J. Hinner, S. J. Marrink, and D. P. Tieleman, “Molecular view of cholesterol flip-flop and chemical potential in different membrane environments,” Journal of the American Chemical Society, vol. 131, no. 35, pp. 12714–12720, 2009.
[42]
H. J. C. Berendsen, D. van der Spoel, and R. van Drunen, “GROMACS: a message-passing parallel molecular dynamics implementation,” Computer Physics Communications, vol. 91, no. 1–3, pp. 43–56, 1995.
[43]
E. Lindahl, B. Hess, and D. van der Spoel, “GROMACS 3.0: a package for molecular simulation and trajectory analysis,” Journal of Molecular Modeling, vol. 7, no. 8, pp. 306–317, 2001.
[44]
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, “GROMACS: fast, flexible, and free,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1701–1718, 2005.
[45]
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “GRGMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation,” Journal of Chemical Theory and Computation, vol. 4, no. 3, pp. 435–447, 2008.
[46]
S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, “THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method,” Journal of Computational Chemistry, vol. 13, no. 8, pp. 1011–1021, 1992.
[47]
J. S. Hub, B. L. de Groot, and D. van der Spoel, “G-whams-a free weighted histogram analysis implementation including robust error and autocorrelation estimates,” Journal of Chemical Theory and Computation, vol. 6, no. 12, pp. 3713–3720, 2010.
[48]
W. Humphrey, A. Dalke, and K. Schulten, “VMD: visual molecular dynamics,” Journal of Molecular Graphics, vol. 14, no. 1, pp. 33–38, 1996.
[49]
K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, “The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling,” Bioinformatics, vol. 22, no. 2, pp. 195–201, 2006.
[50]
F. Kiefer, K. Arnold, M. Künzli, L. Bordoli, and T. Schwede, “The SWISS-MODEL repository and associated resources,” Nucleic Acids Research, vol. 37, no. 1, pp. D387–D392, 2009.
[51]
H. Berendsen, J. Postma, W. van Gunsteren, and J. Hermans, “Interaction models for water in relation to protein hydration,” in Intermolecular Forces, B. Pullman, Ed., vol. 14 of The Jerusalem Symposia on Quantum Chemistry and Biochemistry, pp. 331–342, 1981.
[52]
W. R. P. Scott, P. H. Hünenberger, I. G. Tironi et al., “The GROMOS biomolecular simulation program package,” Journal of Physical Chemistry A, vol. 103, no. 19, pp. 3596–3607, 1999.
[53]
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, “A smooth particle mesh Ewald method,” The Journal of Chemical Physics, vol. 103, no. 19, pp. 8577–8593, 1995.
[54]
D. C. Liu and J. Nocedal, “On the limited memory BFGS method for large scale optimization,” Mathematical Programming B, vol. 45, no. 3, pp. 503–528, 1989.
[55]
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984.
[56]
S. Nose, “A molecular dynamics method for simulations in the canonical ensemble,” Molecular Physics, vol. 52, no. 2, pp. 255–268, 1984.
[57]
W. G. Hoover, “Canonical dynamics: equilibrium phase-space distributions,” Physical Review A, vol. 31, no. 3, pp. 1695–1697, 1985.
[58]
M. Parrinello and A. Rahman, “Polymorphic transitions in single crystals: a new molecular dynamics method,” Journal of Applied Physics, vol. 52, no. 12, pp. 7182–7190, 1981.
[59]
S. Nose and M. L. Klein, “Constant pressure molecular dynamics for molecular systems,” Molecular Physics, vol. 50, pp. 1055–1076, 1983.
[60]
C. Jarzynski, “Nonequilibrium equality for free energy differences,” Physical Review Letters, vol. 78, no. 14, pp. 2690–2693, 1997.
[61]
R. Treisman, “The SRE: a growth factor responsive transcriptional regulator,” Seminars in Cancer Biology, vol. 1, no. 1, pp. 47–58, 1990.
