Exploring the structural features of Aspartate Trans Carbamoylase (TtATCase) from Thermus thermophilus HB8 through in silico approaches: a potential drug target for inborn error of pyrimidine metabolism

References

• Abascal, J. L., & Vega, C. (2005). A general purpose model for the condensed phases of water: TIP4P/2005. Journal of Chemical Physics, 123, 234505–234512.
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402.
   PubMed Web of Science ®Google Scholar
• Bairoch, A., Boeckmann, B., Ferro, S., & Gasteiger, E. (2004). Swiss-Prot: Juggling between evolution and stability. Brief Bioinform, 5, 39–55.
   PubMed Web of Science ®Google Scholar
• Berman, H., Henrick, K., & Nakamura, H. (2003). Announcing the worldwide Protein Data Bank. Nature Structural Biology, 10, –980.
   PubMedGoogle Scholar
• Caroline, D. F. (1969). Pyrimidine synthesis in Neurospora crassa: Gene-enzyme relationships. Journal of Bacteriology, 100, 1371–1377.
   PubMed Web of Science ®Google Scholar
• Chen, P., Van Vliet, F., Van De Casteele, M., Legrain, C., Cunin, R., & Glansdorff, N. (1998). Aspartate transcarbamylase from the hyperthermophilic eubacterium Thermotoga maritima: Fused catalytic and regulatory polypeptides form an allosteric enzyme. Journal of Bacteriology, 180, 6389–6391.
   PubMed Web of Science ®Google Scholar
• Evans, D. R., & Guy, H. I. (2004). Mammalian pyrimidine biosynthesis: Fresh insights into an ancient pathway. Journal of Biological Chemistry, 279, 33035–33038.
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., .., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47, 1739–1749.
   PubMed Web of Science ®Google Scholar
• Grogan, D. W., & Gunsalus, R. P. (1993). Sulfolobus acidocaldarius synthesizes UMP via a standard de novo pathway: results of biochemical-genetic study. Journal of Bacteriology, 175, 1500–1507.
   PubMedGoogle Scholar
• Henne, A., Bruggemann, H., Raasch, C., Wiezer, A., Hartsch, T., Liesegang, H., .., & Fritz, H. J. (2004). The genome sequence of the extreme thermophile Thermus thermophilus. Nature Biotechnology, 22, 547–553.
   PubMed Web of Science ®Google Scholar
• Huang, M., & Graves, L. M. (2003). De novo synthesis of pyrimidine nucleotides; emerging interfaces with signal transduction pathways. Cellular and Molecular Life Sciences, 60, 321–336.
   PubMed Web of Science ®Google Scholar
• 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, 11225–11236.
   Web of Science ®Google Scholar
• Jorgensen, A. M., & Topiol, S. (2008). Driving forces for ligand migration in the leucine transporter. Chemical Biology & Drug Design, 72, 265–272.
   PubMed Web of Science ®Google Scholar
• Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides†. The Journal of Physical Chemistry B, 105, 6474–6487.
   Web of Science ®Google Scholar
• Kevin, J., Edmond, C., Huafeng, X., Ron, O. D., Michael, P. E., Brent, A. G., … David, E. S. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. ACM/IEEE Conference on Supercomputing, ACM, Tampa.
   Google Scholar
• Kontoyianni, M., McClellan, L. M., & Sokol, G. S. (2004). Evaluation of docking performance: Comparative data on docking algorithms. Journal of Medicinal Chemistry, 47, 558–565.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• Loffler, M., Fairbanks, L. D., Zameitat, E., Marinaki, A. M., & Simmonds, H. A. (2005). Pyrimidine pathways in health and disease. Trends in Molecular Medicine, 11, 430–437.
   PubMed Web of Science ®Google Scholar
• Massova, I., & Kollman, P. A. (2000). Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 18, 113–135.
   Google Scholar
• Nakanishi, S., Ito, K., & Tatibana, M. (1968). Two types of carbamyl phosphate synthetase in rat liver: Chromatographic resolution and immunological distinction. Biochemical and Biophysical Research Communications, 33, 774–781.
   PubMed Web of Science ®Google Scholar
• Okazaki, N., Kumei, M., Manzoku, M., Kuramitsu, S., Shirouzu, M., Shinkai, A., & Yokoyama, S. (2007). Structure of a UPF0150-family protein from Thermus thermophilus HB8. Acta Crystallographica Section F-Structural Biology and Crystallization Communications, 63, 173–177.
   PubMedGoogle Scholar
• Pardee, A. B., & Yates, R. A. (1956). Pyrimidine biosynthesis in Escherichia coli. Journal of Biological Chemistry, 221, 743–756.
   PubMedGoogle Scholar
• PyMOL (2010). PyMOL. PyMOL molecular graphics system.
   Google Scholar
• Schrödinger. (2005). Glide: Molecular docking tool, v. 4.0. LLC, New York, Schrodinger.
   Google Scholar
• Schrödinger. (2009a). Ligprep: Ligand preparation tool, v. 2.3. LLC, New York, Schrodinger.
   Google Scholar
• Schrödinger, L. (2009b). Prime, version 2.1. Schrödinger. LLC, New York.
   Google Scholar
• Singh, K., Kirubakaran, P., Nagarajan, S., Sakkiah, S., Muthusamy, K., Velmurgan, D., & Jeyakanthan, J. (2011). Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya virus nsP2 protease. Journal of Molecular Modeling, 18, 39–51.
   PubMed Web of Science ®Google Scholar
• Sippl, M. J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins, 17, 355–362.
   PubMed Web of Science ®Google Scholar
• Stasolla, C., Katahira, R., Thorpe, T. A., & Ashihara, H. (2003). Purine and pyrimidine nucleotide metabolism in higher plants. Journal of Plant Physiology, 160, 1271–1295.
   PubMed Web of Science ®Google Scholar
• Stevens, R. C., Reinisch, K. M., & Lipscomb, W. N. (1991). Molecular structure of Bacillus subtilis aspartate transcarbamoylase at 3.0 A resolution. Proceedings of the National Academy Science of United States of America, 88, 6087–6091.
   PubMedGoogle Scholar
• Van Boxstael, S., Cunin, R., Khan, S., & Maes, D. (2003). Aspartate transcarbamylase from the hyperthermophilic archaeon Pyrococcus abyssi: Thermostability and 1.8A resolution crystal structure of the catalytic subunit complexed with the bisubstrate analogue N-phosphonacetyl-l-aspartate. Journal of Molecular Biology, 326, 203–216.
   PubMedGoogle Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, W407–W410.
   PubMed Web of Science ®Google Scholar
• Zhang, P., Martin, P. D., Purcarea, C., Vaishnav, A., Brunzelle, J. S., Fernando, R., …, & Edwards, B. F. (2009). Dihydroorotase from the hyperthermophile Aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis. Biochemistry, 48, 766–778.
   PubMedGoogle Scholar