Conformational transitions of uracil transporter UraA from Escherichia coli: a molecular simulation study

References

• Alguel, Y., Amillis, S., Leung, J., Lambrinidis, G., Capaldi, S., Scull, N. J., & Byrne, B. (2016). Structure of eukaryotic purine/H+ symporter UapA suggests a role for homodimerization in transport activity. Nature Communications, 7, 11336. doi:10.1038/ncomms11336
   PubMed Web of Science ®Google Scholar
• Almlof, M., Brandsdal, B. O., & Aqvist, J. (2004). Binding affinity prediction with different force fields: Examination of the linear interaction energy method. Journal of Computational Chemistry, 25(10), 1242–1254. doi:10.1002/jcc.20047
   PubMed Web of Science ®Google Scholar
• Almlof, M., Carlsson, J., & Aqvist, J. (2007). Improving the accuracy of the linear interaction energy method for solvation free energies. Journal of Chemical Theory and Computation, 3(6), 2162–2175. doi:10.1021/ct700106b
   PubMed Web of Science ®Google Scholar
• Aqvist, J., Medina, C., & Samuelsson, J. E. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, Design and Selection, 7(3), 385–391. doi:10.1093/protein/7.3.385
   Web of Science ®Google Scholar
• Arakawa, T., Kobayashi-Yurugi, T., Alguel, Y., Iwanari, H., Hatae, H., Iwata, M., & Abe, Y. (2015). Crystal structure of the anion exchanger domain of human erythrocyte band 3. Science, 350(6261), 680–684. doi:10.1126/science.aaa4335
   PubMed Web of Science ®Google Scholar
• Coudray, N., Zhang, Z., Clark, K. M., Ubarretxena, I., Beckstein, O., Dumont, M. E., & Stokes, D. L. (2016). Structure of the Borate Transporter Bor1p by cryo-EM. Biophysical Journal, 110(3), 137A–138A.10.1016/j.bpj.2015.11.785
   Web of Science ®Google Scholar
• Dang, S., Sun, L., Huang, Y., Lu, F., Liu, Y., Gong, H., & Wang, J.. (2010). Structure of a fucose transporter in an outward-open conformation. Nature, 467(7316), 734–738. doi:10.1038/nature09406
   PubMed Web of Science ®Google Scholar
• Fang, Y., Jayaram, H., Shane, T., Kolmakova-Partensky, L., Wu, F., Williams, C., … Miller, C. (2009). Structure of a prokaryotic virtual proton pump at 3.2 angstrom resolution. Nature, 460(7258), 1040–1043. doi: 10.1038/nature08201
   PubMed Web of Science ®Google Scholar
• Georgopoulou, E., Mermelekas, G., Karena, E., & Frillingos, S. (2010). Purine substrate recognition by the nucleobase-ascorbate transporter signature motif in the YgfO xanthine permease ASN-325 binds and ALA-323 senses substrate. Journal of Biological Chemistry, 285(25), 19422–19433. doi:10.1074/jbc.M110.120543
   PubMed Web of Science ®Google Scholar
• Gournas, C., Papageorgiou, I., & Diallinas, G. (2008). The nucleobase-ascorbate transporter (NAT) family: Genomics, evolution, structure-function relationships and physiological role. Molecular BioSystems, 4(5), 404–416. doi:10.1039/b719777b
   PubMed Web of Science ®Google Scholar
• Kandt, C., Ash, W. L., & Tieleman, D. P. (2007). Setting up and running molecular dynamics simulations of membrane proteins. Methods, 41(4), 475–488. doi:10.1016/j.ymeth.2006.08.006
   PubMed Web of Science ®Google Scholar
• Karena, E., & Frillingos, S. (2011). The role of transmembrane segment TM3 in the xanthine permease XanQ of Escherichia coli. Journal of Biological Chemistry, 286(45), 39595–39605. doi:10.1074/jbc.M111.299164
   PubMed Web of Science ®Google Scholar
• Karena, E., Tatsaki, E., Lambrinidis, G., Mikros, E., & Frillingos, S. (2015). Analysis of conserved NCS2 motifs in the Escherichia coli xanthine permease XanQ. Molecular Microbiology, 98(3), 502–517. doi:10.1111/mmi.13138
   PubMed Web of Science ®Google Scholar
• Kozmin, S. G., Stepchenkova, E. I., Chow, S. C., & Schaaper, Roel M. (2013). A critical role for the putative NCS2 nucleobase permease YjcD in the sensitivity of Escherichia coli to cytotoxic and mutagenic purine analogs. Mbio, 4(6), 00661-13. doi:10.1128/mBio.00661-13
   Web of Science ®Google Scholar
• Lansangan, J. R. G., & Barrios, E. B. (2009). Principal components analysis of nonstationary time series data. Statistics and Computing, 19(2), 173–187. doi:10.1007/s11222-008-9082-y
   Web of Science ®Google Scholar
• Lu, F., Li, S., Jiang, Y., Jiang, J., Fan, H., Lu, G., & Deng, D. (2011). Structure and mechanism of the uracil transporter UraA. Nature, 472(7342), 243–246. doi:10.1038/nature09885
   PubMed Web of Science ®Google Scholar
• Nosé, S., & Klein, M. L. (2006). Constant pressure molecular dynamics for molecular systems. Molecular Physics, 50(5), 1055–1076. doi:10.1080/00268978300102851
   Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. doi:10.1063/1.328693
   Web of Science ®Google Scholar
• Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854. doi: 10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Ressl, S., van Scheltinga, A. C. T., Vonrhein, C., Ott, V., & Ziegler, C. (2009). Molecular basis of transport and regulation in the Na+/betaine symporter BetP. Nature, 458(7234), 47–52. doi:10.1038/nature07819
   PubMed Web of Science ®Google Scholar
• Saier, M. H., Eng, B. H., Fard, S., Garg, J., Haggerty, D. A., Hutchinson, W. J., & Jack, D. L. (1999). Phylogenetic characterization of novel transport protein families revealed by genome analyses. Biochimica et Biophysica Acta (BBA) – Reviews on Biomembranes, 1422(1), 1–56. doi:10.1016/s0304-4157(98)00023-9
   PubMed Web of Science ®Google Scholar
• Savini, I., Rossi, A., Pierro, C., Avigliano, L., & Catani, M. V. (2008). SVCT1 and SVCT2: Key proteins for vitamin C uptake. Amino Acids, 34(3), 347–355. doi:10.1007/s00726-007-0555-7
   PubMed Web of Science ®Google Scholar
• Schuttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D-Biological Crystallography, 60, 1355–1363. doi:10.1107/s0907444904011679
   PubMed Web of Science ®Google Scholar
• Smart, O. S., Goodfellow, J. M., & Wallace, B. A. (1993). The pore dimensions of gramicidin A. Biophysical Journal, 65(6), 2455–2460.10.1016/S0006-3495(93)81293-1
   PubMed Web of Science ®Google Scholar