References
- Agarwal, P. K. (2005). Role of protein dynamics in reaction rate enhancement by enzymes. Journal of the American Chemical Society, 127(43), 15248–15256. doi:10.1021/ja055251s. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/16248667
- Agyeman, A. A., & Ofori-Asenso, R. (2017). Tuberculosis – an overview. Journal of Public Health and Emergency, 1, 7. doi:10.21037/jphe.2016.12.08
- Artymiuk, P. J., Blake, C. C., Grace, D. E., Oatley, S. J., Phillips, D. C., & Sternberg, M. J. (1979). Crystallographic studies of the dynamic properties of lysozyme. Nature, 280(5723), 563–568. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/460438
- Awasthi, D., Kumar, K., Knudson, S. E., Slayden, R. A., & Ojima, I. (2013). SAR studies on trisubstituted benzimidazoles as inhibitors of Mtb FtsZ for the development of novel antitubercular agents. Journal of Medicinal Chemistry, 56(23), 9756–9770. doi:10.1021/jm401468w. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/24266862
- Ballu, S., Itteboina, R., Sivan, S. K., & Manga, V. (2018). Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. Journal of Receptors and Signal Transduction, 38(1), 61–70. doi:10.1080/10799893.2018.1426607. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/29369011
- Becke, A. D. (1993). Density‐functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98(7), 5648–5652. doi:10.1063/1.464913. Retrieved from https://aip.scitation.org/doi/abs/10.1063/1.464913
- Chong, S.-H., Chatterjee, P., & Ham, S. (2017). Computer simulations of intrinsically disordered proteins. Annual Review of Physical Chemistry, 68, 117–134. doi:10.1146/annurev-physchem-052516-050843
- Daniel, R. M., Dines, M., & Petach, H. H. (1996). The denaturation and degradation of stable enzymes at high temperatures. Biochemical Journal, 317(1), 1–11. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8694749
- Dosztanyi, Z., Csizmok, V., Tompa, P., & Simon, I. (2005). IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21(16), 3433–3434. doi:10.1093/bioinformatics/bti541. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/15955779
- Dunker, A. K., Lawson, J. D., Brown, C. J., Williams, R. M., Romero, P., Oh, J. S., … Obradovic, Z. (2001). Intrinsically disordered protein. Journal of Molecular Graphics and Modelling, 19(1), 26–59. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11381529
- Dunker, A. K., Obradovic, Z., Romero, P., Garner, E. C., & Brown, C. J. (2000). Intrinsic protein disorder in complete genomes. Genome Informatics Service Workshop on Genome Informatics, 11, 161–171. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11700597
- Eisenmesser, E. Z., Millet, O., Labeikovsky, W., Korzhnev, D. M., Wolf-Watz, M., Bosco, D. A., … Kern, D. (2005). Intrinsic dynamics of an enzyme underlies catalysis. Nature, 438(7064), 117–121. doi:10.1038/nature04105. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/16267559
- Frauenfelder, H., Petsko, G. A., & Tsernoglou, D. (1979). Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature, 280(5723), 558–563. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/460437
- Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R. … Fox, D. J. (2016). Gaussian 9. Wallingford, CT: Gaussian, Inc.
- Fukui, K. (1982). Role of frontier orbitals in chemical reactions. Science, 218(4574), 747–754. doi:10.1126/science.218.4574.747. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/17771019
- Grant, B. J., Rodrigues, A. P., ElSawy, K. M., McCammon, J. A., & Caves, L. S. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22(21), 2695–2696. doi:10.1093/bioinformatics/btl461. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/16940322
- Haranahalli, K., Tong, S., & Ojima, I. (2016). Recent advances in the discovery and development of antibacterial agents targeting the cell-division protein FtsZ. Bioorganic & Medicinal Chemistry, 24(24), 6354–6369. doi:10.1016/j.bmc.2016.05.003. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/27189886
- Hong, W., Deng, W., & Xie, J. (2013). The structure, function, and regulation of Mycobacterium FtsZ. Cell Biochemistry and Biophysics, 65(2), 97–105. doi:10.1007/s12013-012-9415-5. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22932926
- Huang, Q., Tonge, P. J., Slayden, R. A., Kirikae, T., & Ojima, I. (2007). FtsZ: A novel target for tuberculosis drug discovery. Current Topics in Medicinal Chemistry, 7(5), 527–543. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/17346197
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8744570
- Hurley, K. A., Santos, T. M., Nepomuceno, G. M., Huynh, V., Shaw, J. T., & Weibel, D. B. (2016). Targeting the bacterial division protein FtsZ. Journal of Medicinal Chemistry, 59(15), 6975–6998. doi:10.1021/acs.jmedchem.5b01098. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/26756351
- Ishida, T., & Kinoshita, K. (2007). PrDOS: Prediction of disordered protein regions from amino acid sequence. Nucleic Acids Research, 35(Web Server), W460–W464. doi:10.1093/nar/gkm363. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/17567614
- Islam, M. M., Hameed, H. M. A., Mugweru, J., Chhotaray, C., Wang, C., Tan, Y., … Zhang, T. (2017). Drug resistance mechanisms and novel drug targets for tuberculosis therapy. Journal of Genetics and Genomics, 44(1), 21–37. doi:10.1016/j.jgg.2016.10.002. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/28117224
- Jaiswal, R., & Panda, D. (2008). Cysteine 155 plays an important role in the assembly of Mycobacterium tuberculosis FtsZ. Protein Science, 17(5), 846–854. doi:10.1110/ps.083452008. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/18436955
- Jamous, C., Basdevant, N., & Ha-Duong, T. (2014). Influence of GTP/GDP and magnesium ion on the solvated structure of the protein FtsZ: A molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 32(6), 916–927. doi:10.1080/07391102.2013.799436. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/23782014
- Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. doi:10.1063/1.445869. Retrieved from https://aip.scitation.org/doi/abs/10.1063/1.445869
- Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. doi:10.1021/ja9621760. Retrieved from https://doi.org/10.1021/ja9621760
- Jorgensen, W. L., & Tirado-Rives, J. (1988). The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110(6), 1657–1666. doi:10.1021/ja00214a001. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/27557051
- Kumar, K., Awasthi, D., Berger, W. T., Tonge, P. J., Slayden, R. A., & Ojima, I. (2010). Discovery of anti-TB agents that target the cell-division protein FtsZ. Future Medicinal Chemistry, 2(8), 1305–1323. doi:10.4155/fmc.10.220. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/21339840
- Leung, A. K., Lucile White, E., Ross, L. J., Reynolds, R. C., DeVito, J. A., & Borhani, D. W. (2004). Structure of Mycobacterium tuberculosis FtsZ reveals unexpected, G protein-like conformational switches. Journal of Molecular Biology, 342(3), 953–970. doi:10.1016/j.jmb.2004.07.061. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/15342249
- Li, D., Chi, B., Wang, W.-W., Gao, J.-M., & Wan, J. (2017). Exploring the possible binding mode of trisubstituted benzimidazoles analogues in silico for novel drug design targeting Mtb FtsZ. Medicinal Chemistry Research, 26(1), 153–169. doi:10.1007/s00044-016-1734-4. Retrieved from https://doi.org/10.1007/s00044-016-1734-4
- Li, X., & Ma, S. (2015). Advances in the discovery of novel antimicrobials targeting the assembly of bacterial cell division protein FtsZ. European Journal of Medicinal Chemistry, 95, 1–15. doi:10.1016/j.ejmech.2015.03.026. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/25791674
- Li, X., Romero, P., Rani, M., Dunker, A. K., & Obradovic, Z. (1999). Predicting protein disorder for N-, C-, and internal regions. Genome Informatics Service Workshop on Genome Informatics, 10, 30–40. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11072340
- Mao, Y., & Zhang, Y. (2012). Thermal conductivity, shear viscosity and specific heat of rigid water models. Chemical Physics Letters, 542, 37–41. doi:https://doi.org/10.1016/j.cplett.2012.05.044. Retrieved from http://www.sciencedirect.com/science/article/pii/S0009261412006367
- Margolin, W. (2005). FtsZ and the division of prokaryotic cells and organelles. Nature Reviews Molecular Cell Biology, 6(11), 862–871. doi:10.1038/nrm1745. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/16227976 doi:10.1038/nrm1745
- Martin-Galiano, A. J., Buey, R. M., Cabezas, M., & Andreu, J. M. (2010). Mapping flexibility and the assembly switch of cell division protein FtsZ by computational and mutational approaches. Journal of Biological Chemistry, 285(29), 22554–22565. doi:10.1074/jbc.M110.117127. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/20472561
- Matsui, T., Han, X., Yu, J., Yao, M., & Tanaka, I. (2014). Structural change in FtsZ induced by intermolecular interactions between bound GTP and the T7 loop. Journal of Biological Chemistry, 289(6), 3501–3509. doi:10.1074/jbc.M113.514901. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/24347164
- Matsui, T., Yamane, J., Mogi, N., Yamaguchi, H., Takemoto, H., Yao, M., & Tanaka, I. (2012). Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus. Acta Crystallographica Section D Biological Crystallography, 68(9), 1175–1188. doi:10.1107/S0907444912022640. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22948918
- Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., … Gough, J. (2013). D(2)P(2): Database of disordered protein predictions. Nucleic Acids Research, 41(D1), D508–D516. doi:10.1093/nar/gks1226. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/23203878
- Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., & Dunker, A. K. (2005). Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins: Structure, Function, and Bioinformatics, 61(S7), 176–182. doi:10.1002/prot.20735. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/16187360
- W. H. Organisation. (2015). Retrieved Date.
- Park, B., Awasthi, D., Chowdhury, S. R., Melief, E. H., Kumar, K., Knudson, S. E., … Ojima, I. (2014). Design, synthesis and evaluation of novel 2,5,6-trisubstituted benzimidazoles targeting FtsZ as antitubercular agents. Bioorganic & Medicinal Chemistry, 22(9), 2602–2612. doi:10.1016/j.bmc.2014.03.035. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/24726304
- Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K., & Obradovic, Z. (2006). Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics, 7(1), 208. doi:10.1186/1471-2105-7-208. Retrieved from https://doi.org/10.1186/1471-2105-7-208
- Peng, Z., Yan, J., Fan, X., Mizianty, M. J., Xue, B., Wang, K., … Kurgan, L. (2015). Exceptionally abundant exceptions: Comprehensive characterization of intrinsic disorder in all domains of life. Cellular and Molecular Life Sciences, 72(1), 137–151. doi:10.1007/s00018-014-1661-9. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/24939692
- Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., & Dunker, A. K. (2001). Sequence complexity of disordered protein. Proteins, 42(1), 38–48. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11093259
- Ruiz-Avila, L. B., Huecas, S., Artola, M., Vergoñós, A., Ramírez-Aportela, E., Cercenado, E., … Andreu, J. M. (2013). Synthetic inhibitors of bacterial cell division targeting the GTP-binding site of FtsZ. ACS Chemical Biology, 8(9), 2072–2083. doi:10.1021/cb400208z. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/23855511
- Scheffers, D. J., de Wit, J. G., den Blaauwen, T., & Driessen, A. J. (2002). GTP hydrolysis of cell division protein FtsZ: Evidence that the active site is formed by the association of monomers. Biochemistry, 41(2), 521–529. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11781090
- Shan, Y., Eastwood, M. P., Zhang, X., Kim, E. T., Arkhipov, A., Dror, R. O., … Shaw, D. E. J. C. (2012). Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell, 149(4), 860–870. doi:10.1016/j.cell.2012.02.063
- Singh, I., Singh, S., Verma, V., Uversky, V. N., & Chandra, R. (2017). In silico evaluation of the resistance of the T790M variant of epidermal growth factor receptor kinase to cancer drug Erlotinib. Journal of Biomolecular Structure and Dynamics, 1–11. doi:10.1080/07391102.2017.1411293
- Sloan, D. J., & Lewis, J. M. (2016). Management of multidrug-resistant TB: Novel treatments and their expansion to low resource settings. Transactions of the Royal Society of Tropical Medicine and Hygiene, 110(3), 163–172. doi:10.1093/trstmh/trv107. Retrieved from http://dx.doi.org/10.1093/trstmh/trv107
- Sun, N., Chan, F.-Y., Lu, Y.-J., Neves, M. A. C., Lui, H.-K., Wang, Y., … Wong, K.-Y. (2014). Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity. PLoS One, 9(5), e97514. doi:10.1371/journal.pone.0097514. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/24824618
- Sunnetcioglu, A., Sunnetcioglu, M., Binici, I., Baran, A. I., Karahocagil, M. K., & Saydan, M. R. (2015). Comparative analysis of pulmonary and extrapulmonary tuberculosis of 411 cases. Annals of Clinical Microbiology and Antimicrobials, 14(1), 34.
- Tang, K. E., & Dill, K. A. (1998). Native protein fluctuations: The conformational-motion temperature and the inverse correlation of protein flexibility with protein stability. Journal of Biomolecular Structure and Dynamics, 16(2), 397–411. doi:10.1080/07391102.1998.10508256. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/9833677
- Uversky, V. N. (2013). Unusual biophysics of intrinsically disordered proteins. Biochimica et Biophysica Acta, 1834(5), 932–951. doi:10.1016/j.bbapap.2012.12.008. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/23269364
- Uversky, V. N. (2017). How to predict disorder in a protein of interest. Methods in Molecular Biology (Clifton, N.J.), 1484, 137–158. doi:10.1007/978-1-4939-6406-2_11. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/27787825
- Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000). Why are “natively unfolded” proteins unstructured under physiologic conditions?. Proteins: Structure, Function, and Genetics, 41(3), 415–427. doi:10.1002/1097-0134(20001115)41:3<415::AID-PROT130 > 3.0.CO;2-7. Retrieved from https://onlinelibrary.wiley.com/doi/abs/10.1002/1097-0134%2820001115%2941%3A3%3C415%3A%3AAID-PROT130%3E3.0.CO%3B2-7
- Varley, P. G., & Pain, R. H. (1991). Relation between stability, dynamics and enzyme activity in 3-phosphoglycerate kinases from yeast and Thermus thermophilus. Journal of Molecular Biology, 220(2), 531–538. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/1856872 doi:10.1016/0022-2836(91)90028-5
- Wagner, G., & Wuthrich, K. (1979). Correlation between the amide proton exchange rates and the denaturation temperatures in globular proteins related to the basic pancreatic trypsin inhibitor. Journal of Molecular Biology, 130(1), 31–37. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/469937 doi:10.1016/0022-2836(79)90550-3
- Walsh, I., Martin, A. J., Di Domenico, T., & Tosatto, S. C. (2012). ESpritz: Accurate and fast prediction of protein disorder. Bioinformatics, 28(4), 503–509. doi:10.1093/bioinformatics/btr682. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22190692
- Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., & Jones, D. T. (2004). Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. Journal of Molecular Biology, 337(3), 635–645. doi:10.1016/j.jmb.2004.02.002. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/15019783
- Williams, P. D., Pollock, D. D., & Goldstein, R. A. (2007). Functionality and the evolution of marginal stability in proteins: Inferences from lattice simulations. Evolutionary Bioinformatics Online, 2, 91–101. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/19455204
- Wrba, A., Schweiger, A., Schultes, V., Jaenicke, R., & Zavodszky, P. (1990). Extremely thermostable D-glyceraldehyde-3-phosphate dehydrogenase from the eubacterium Thermotoga maritima. Biochemistry, 29(33), 7584–7592. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/2271518 doi:10.1021/bi00485a007
- Wright, P. E., & Dyson, H. J. (1999). Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. Journal of Molecular Biology, 293(2), 321–331. doi:10.1006/jmbi.1999.3110. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/10550212 doi:10.1006/jmbi.1999.3110
- Xue, B., Dunbrack, R. L., Williams, R. W., Dunker, A. K., & Uversky, V. N. (2010). PONDR-FIT: A meta-predictor of intrinsically disordered amino acids. Biochimica et Biophysica Acta, 1804(4), 996–1010. doi:10.1016/j.bbapap.2010.01.011. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/20100603
- Xue, B., Dunker, A. K., & Uversky, V. N. (2012). Orderly order in protein intrinsic disorder distribution: Disorder in 3500 proteomes from viruses and the three domains of life. Journal of Biomolecular Structure and Dynamics, 30(2), 137–149. doi:10.1080/07391102.2012.675145. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22702725