References
- Baldus, J. M., Green, B. D., Youngman, P., & Moran, C. P. Jr.(1994). Phosphorylation of Bacillus subtilis transcription factor Spo0A stimulates transcription from the spoIIG promoter by enhancing binding to weak 0A boxes. Journal of Bacteriology, 176(2), 296–306. doi:10.1128/jb.176.2.296-306.1994
- Banse, A. V., Hobbs, E. C., & Losick, R. (2011). Phosphorylation of Spo0A by the Histidine Kinase KinD Requires the Lipoprotein Med in Bacillus subtilis. Journal of Bacteriology, 193 (15), 3949–3955. doi:10.1128/JB.05199-11
- Bogusz, S., Cheatham, T. E., & Brooks, B. R. (1998). Removal of pressure and free energy artefacts in charged periodic systems via net charge corrections to the ewald potential. Journal of Chemical Physics, 108 (17), 7070–7084. doi:10.1063/1.476320
- Brooks, B., Brooks, C. L., III, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614. doi:10.1002/jcc.21287
- Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., & Karplus, M. (1983). Charmm: A program for macromolecular energy, minimization, and molecular dynamics calculations. Journal of Computational Chemistry, 4, 18–217.
- Burbulys, D., Trach, K. A., & Hoch, J. A. (1991). The initiation of sporulation in Bacillus subtilis is controlled by a multicomponent phosphorelay. Cell, 64 (3), 545–552. doi:10.1016/0092-8674(91)90238-T
- Chastanet, A., & Losick, R. (2011). Just-in-Time Control of Spo0A Synthesis in Bacillus subtilis by Multiple Regulatory Mechanisms. Journal of Bacteriology, 193 (22), 6366–6374. doi:10.1128/JB.06057-11
- Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
- Hummer, G., Pratt, L., & Garcia, A. (1996). Free energy of ionic hydration. The Journal of Physical Chemistry, 100(4), 1206–1215. doi:10.1021/jp951011v
- Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics., 79 (2), 926–935. doi:10.1063/1.445869
- Mackerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J., Field, M. J., … Karplus, M. (1998). An all-atom empirical potential for molecular modelling and dynamics study of proteins. The Journal of Physical Chemistry B, 102 (18), 3586–3616. doi:10.1021/jp973084f
- Mackerell, A. D., Wiorkiewicz-Kuczera, J., & Karplus, M. (1995). An all-atom empirical energy forcefield for the study of nucleic acids. Journal of the American Chemical Society, 117 (48), 11946–11975. doi:10.1021/ja00153a017
- Molle, V., Fujita, M., Jensen, S. T., Patrick, E., González-Pastor, J. E., Liu, J. S., & Losick, R. (2003). The Spo0A regulon of Bacillus subtilis. Molecular Microbiology, 50 (5), 1683–1701. doi:10.1046/j.1365-2958.2003.03818.x
- Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26 (16), 1781–1802. doi:10.1002/jcc.20289
- Rosenbusch, K. E., Bakker, D., Kuijper, E. J., & Smits, W. K. (2012). C. difficile 630Δerm Spo0A regulates sporulation, but does not contribute to toxin production, by direct high-affinity binding to target DNA. PloS One, 7 (10), e48608. doi:10.1371/journal.pone.0048608
- Satola, S., Kirchman, P. A., & Moran, C. P. Jr.(1991). Spo0A binds to a promoter used by sigma A RNA polymerase during sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences, 88(10), 4533–4537. doi:10.1073/pnas.88.10.4533
- Webb, B., & Sali, A. (2016). Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics, 54, 5.6.1–5.6.37.
- York, K., Kenney, T. J., Satola, S., Moran, C. P., Jr., Poth, H., & Youngman, P. (1992). Spo0A controls the sigma A-dependent activation of Bacillus subtilis sporulation-specific transcription unit spoIIE. Journal of Bacteriology, 174(8), 2648–26458. doi:10.1128/jb.174.8.2648-2658.1992
- Zhao, H., Msadek, T., Zapf, J. W., Madhusudan, Hoch, J. A., & Varughese, K. I. (2002). DNA Complexed structure of the key transcription factor initiating development in sporulating bacteria. Structure, 10, 1041–1050.