References
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/https://doi.org/10.1016/j.softx.2015.06.001
- Aldeghi, M., Ross, G. A., Bodkin, M. J., Essex, J. W., Knapp, S., & Biggin, P. C. (2008). Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. Communications Chemistry., 1, 19.
- Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/https://doi.org/10.1093/nar/28.1.235
- Bingöl, E. N., Serçinoğlu, O., & Ozbek, P. (2019). How do mutations and allosteric inhibitors modulate caspase-7 activity? A molecular dynamics study. Journal of Biomolecular Structure & Dynamics, 37(13), 3456–3466. https://doi.org/https://doi.org/10.1080/07391102.2018.1517611
- Boatright, K. M., & Salvesen, G. S. (2003). Mechanisms of caspase activation. Current Opinion in Cell Biology, 15(6), 725–731. https://doi.org/https://doi.org/10.1016/j.ceb.2003.10.009
- Cao, Q., Wang, X. J., Liu, C. W., Liu, D. F., Li, L. F., Gao, Y. Q., & Su, X. D. (2012). Inhibitory mechanism of caspase-6 phosphorylation revealed by crystal structures, molecular dynamics simulations, and biochemical assays. The Journal of Biological Chemistry, 287(19), 15371–15379. https://doi.org/https://doi.org/10.1074/jbc.M112.351213
- Capdevila, D. A., Edmonds, K. A., Campanello, G. C., Wu, H., Gonzalez-Gutierrez, G., & Giedroc, D. P. (2018). Functional role of solvent entropy and conformational entropy of metal binding in a dynamically driven allosteric system. Journal of the American Chemical Society, 140(29), 9108–9119. https://doi.org/https://doi.org/10.1021/jacs.8b02129
- Caro, J. A., Harpole, K. W., Kasinath, V., Lim, J., Granja, J., Valentine, K. G., Sharp, K. A., & Wand, A. J. (2017). Entropy in molecular recognition by proteins. Proceedings of the National Academy of Sciences of the United States of America, 114(25), 6563–6568. https://doi.org/https://doi.org/10.1073/pnas.1621154114
- Chai, J., Wu, Q., Shiozaki, E., Srinivasula, S. M., Alnemri, E. S., & Shi, Y. (2001). Crystal structure of a procaspase-7 zymogen: Mechanisms of activation and substrate binding. Cell, 107(3), 399–407. https://doi.org/https://doi.org/10.1016/s0092-8674(01)00544-x
- Chang, H. Y., & Yang, X. (2000). Proteases for cell suicide: Functions and regulation of caspases. Microbiology and Molecular Biology Reviews , 64(4), 821–846. https://doi.org/https://doi.org/10.1128/mmbr.64.4.821-846.2000
- Creagh, E. M. (2014). Caspase crosstalk: Integration of apoptotic and innate immune signalling pathways. Trends in Immunology, 35(12), 631–640. https://doi.org/https://doi.org/10.1016/j.it.2014.10.004
- Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log (N) method for Ewald sums in large systems. Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/https://doi.org/10.1063/1.464397
- Donepudi, M., & Grütter, M. G. (2002). Structure and zymogen activation of caspases. Biophysical Chemistry, 101–102, 145–153. https://doi.org/https://doi.org/10.1016/S0301-4622(02)00151-5
- Elliott, J. M., Rouge, L., Wiesmann, C., & Scheer, J. M. (2009). Crystal structure of procaspase-1 zymogen domain reveals insight into inflammatory caspase autoactivation. The Journal of Biological Chemistry, 284(10), 6546–6553. https://doi.org/https://doi.org/10.1074/jbc.M806121200
- Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/https://doi.org/10.1063/1.470117
- Fuchs, J. E., von Grafenstein, S., Huber, R. G., Wallnoefer, H. G., & Liedl, K. R. (2014). Specificity of a protein-protein interface: Local dynamics direct substrate recognition of effector caspases. Proteins, 82(4), 546–555. https://doi.org/https://doi.org/10.1002/prot.24417
- Fuentes-Prior, P., & Salvesen, G. S. (2004). The protein structures that shape caspase activity, specificity, activation and inhibition. The Biochemical Journal, 384(Pt 2), 201–232. https://doi.org/https://doi.org/10.1042/BJ20041142
- Gogoi, P., & Kanaujia, S. P. (2019). Role of structural features in oligomerization, active-site integrity and ligand binding of ribose-1,5-bisphosphate isomerase . Computational and Structural Biotechnology Journal, 17, 333–344. https://doi.org/https://doi.org/10.1016/j.csbj.2019.02.009
- Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation, 4(1), 116–122. https://doi.org/https://doi.org/10.1021/ct700200b
- Kanaujia, S. P., & Sekar, K. (2009). Structural and functional role of water molecules in bovine pancreatic phospholipase A(2): A data-mining approach. Acta Crystallographica. Section D, Biological Crystallography, 65(Pt 1), 74–84. https://doi.org/https://doi.org/10.1107/S0907444908039292
- Kearney, B. M., Schwabe, M., Marcus, K. C., Roberts, D. M., Dechene, M., Swartz, P., & Mattos, C. (2020). DRoP: Automated detection of conserved solvent-binding sites on proteins. Proteins, 88(1), 152–165. https://doi.org/https://doi.org/10.1002/prot.25781
- Maciag, J. J., Mackenzie, S. H., Tucker, M. B., Schipper, J. L., Swartz, P., & Clark, A. C. (2016). Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection. Proceedings of the National Academy of Sciences of the United states of America, 113(41), E6080–E6088. https://doi.org/https://doi.org/10.1073/pnas.1603549113
- Mariathasan, S., & Monack, D. M. (2007). Inflammasome adaptors and sensors: Intracellular regulators of infection and inflammation. Nature Reviews. Immunology, 7(1), 31–40. https://doi.org/https://doi.org/10.1038/nri1997
- Martinon, F., Burns, K., & Tschopp, J. (2002). The inflammasome: A molecular platform triggering activation of inflammatory caspases and processing of proIL-beta. Molecular Cell, 10(2), 417–426. https://doi.org/https://doi.org/10.1016/s1097-2765(02)00599-3
- McIlwain, D. R., Berger, T., & Mak, T. W. (2013). Caspase functions in cell death and disease. Cold Spring Harbor Perspectives in Biology, 5(4), a008656 https://doi.org/https://doi.org/10.1101/cshperspect.a008656
- Muzio, M., Stockwell, B. R., Stennicke, H. R., Salvesen, G. S., & Dixit, V. M. (1998). An induced proximity model for caspase-8 activation. Journal of Biological Chemistry, 273(5), 2926–2930. https://doi.org/https://doi.org/10.1074/jbc.273.5.2926
- Nucci, N. V., Pometun, M. S., & Wand, A. J. (2011). Site-resolved measurement of water-protein interactions by solution NMR. Nature Structural & Molecular Biology, 18(2), 245–249. https://doi.org/https://doi.org/10.1038/nsmb.1955
- Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/https://doi.org/10.1063/1.328693
- Petrilli, V., Dostert, C., Muruve, D. A., & Tschopp, J. (2007). The inflammasome: A danger sensing complex triggering innate immunity. Current Opinion in Immunology, 19(6), 615–622. https://doi.org/https://doi.org/10.1016/j.coi.2007.09.002
- Petrilli, V., Papin, S., & Tschopp, J. (2005). The inflammasome. Current Biology, 15(15), R581. https://doi.org/https://doi.org/10.1016/j.cub.2005.07.049
- Ponder, J. W., & Case, D. A. (2003). Force fields for protein simulations. Advances in Protein Chemistry. 66, 27–85. https://doi.org/https://doi.org/10.1016/s0065-3233(03)66002-x
- Pop, C., & Salvesen, G. S. (2009). Human caspases: Activation, specificity, and regulation. Journal of Biological Chemistry, 284(33), 21777–21781. https://doi.org/https://doi.org/10.1074/jbc.R800084200
- Riedl, S. J., & Shi, Y. (2004). Molecular mechanisms of caspase regulation during apoptosis. Nature Reviews. Molecular Cell Biology, 5(11), 897–907. https://doi.org/https://doi.org/10.1038/nrm1496
- Romanowski, M. J., Scheer, J. M., O'Brien, T., & McDowell, R. S. (2004). Crystal structures of a ligand-free and malonate-bound human caspase-1: Implications for the mechanism of substrate binding. Structure (London, England : 1993), 12(8), 1361–1371. https://doi.org/https://doi.org/10.1016/j.str.2004.05.010
- Shi, Y. (2002). Mechanisms of caspase activation and inhibition during apoptosis. Molecular Cell, 9(3), 459–470. https://doi.org/https://doi.org/10.1016/s1097-2765(02)00482-3
- Teze, D., Hendrickx, J., Dion, M., Tellier, C., Woods, V. L., Jr. Tran, V., & Sanejouand, Y.-H. (2013). Conserved water molecules in family 1 glycosidases: A DXMS and molecular dynamics study. Biochemistry, 52(34), 5900–5910. https://doi.org/https://doi.org/10.1021/bi400260b
- Tschopp, J., Martinon, F., & Burns, K. (2003). NALPs: A novel protein family involved in inflammation. Nature Reviews. Molecular Cell Biology, 4(2), 95–104. https://doi.org/https://doi.org/10.1038/nrm1019
- Walker, N. P., Talanian, R. V., Brady, K. D., Dang, L. C., Bump, N. J., Ferenza, C. R., Franklin, S., Ghayur, T., Hackett, M. C., Hammill, L. D., & Herzog, L. (1994). Crystal structure of the cysteine protease interleukin-1β-converting enzyme: A (p20/p10) 2 homodimer. Cell, 78(2), 343–352. https://doi.org/https://doi.org/10.1016/0092-8674(94)90303-4
- Wilson, K. P., Black, J. A., Thomson, J. A., Kim, E. E., Griffith, J. P., Navia, M. A., Murcko, M. A., Chambers, S. P., Aldape, R. A., Raybuck, S. A., & Livingston, D. J. (1994). Structure and mechanism of interleukin-1 beta converting enzyme . Nature, 370(6487), 270–275. https://doi.org/https://doi.org/10.1038/370270a0