Molecular dynamics simulation of human urea transporter B

References

• Hediger MA, Smith CP, You G, et al. Structure, regulation and physiological roles of urea transporters. Kidney Int. 1996;49:1615–1623.
   PubMed Web of Science ®Google Scholar
• Klein JD, Blount MA, Sands JM. Urea transport in the kidney. Compr Physiol. 2011;1:699–729.
   PubMed Web of Science ®Google Scholar
• Sands JM. Mammalian urea transporters. Annu Rev Physiol. 2003;65:543–566.
   PubMed Web of Science ®Google Scholar
• Yang B, Sands MJ. Urea transporters. Dordrecht: Springer Netherlands; 2014.
   Google Scholar
• Esteva-Font C, Anderson MO, Verkman AS. Urea transporter proteins as targets for small-molecule diuretics. Nat Rev Nephrol. 2015;11:113–123.
   PubMed Web of Science ®Google Scholar
• Smith CP. Mammalian urea transporters. Exp Physiol. 2009;94:180–185.
   PubMed Web of Science ®Google Scholar
• Zhao D, Sonawane ND, Levin MH, et al. Comparative transport efficiencies of urea analogues through urea transporter UT-B. Biochim Biophys Acta. 2007;1768:1815–1821.
   PubMed Web of Science ®Google Scholar
• Levin EJ, Cao Y, Enkavi G, et al. Structure and permeation mechanism of a mammalian urea transporter. Proc Natl Acad Sci U S A. 2012;109:11194–9.
   PubMed Web of Science ®Google Scholar
• Geyer RR, Musa-Aziz R, Enkavi G, et al. Movement of NH3through the human urea transporter B: a new gas channel. Am J Physiol Renal Physiol. 2013;304:F1447–F1457.
   PubMed Web of Science ®Google Scholar
• Azouzi S, Gueroult M, Ripoche P, et al. Energetic and molecular water permeation mechanisms of the human red blood cell urea transporter B. PLoS One. 2013;8:e82338.
   PubMed Web of Science ®Google Scholar
• Ariz-Extreme I, Hub JS. Potential of mean force calculations of solute permeation across UT-B and AQP1: a comparison between molecular dynamics and 3D-RISM. J Phys Chem B. 2017;121:1506–1519.
   PubMed Web of Science ®Google Scholar
• Dietz L, Chi G, Pike ACW, et al. 6QD5 X-ray structure of the human urea channel SLC14A1/UT1 to be published. Released: 1/9/2019.
   Google Scholar
• Aoun M, Corsetto PA, Nugue G, et al. Changes in red blood cell membrane lipid composition: a new perspective into the pathogenesis of PKAN. Mol Genet Metabol. 2017;121:180–189.
   PubMed Web of Science ®Google Scholar
• Virtanen JA, Cheng KH, Somerharju P. Phospholipid composition of the mammalian red cell membrane can be rationalized by a superlattice model. Proc Natl Acad Sci U S A. 1998;95:4964–4969.
   PubMed Web of Science ®Google Scholar
• Jo S, Kim T, Iyer VG, et al. CHARMM-GUI: a web- based graphical user interface for CHARMM. J Comput Chem. 2008;29:1859–1865.
   PubMed Web of Science ®Google Scholar
• Wu EL, Cheng X, Jo S, et al. CHARMM-GUI membrane builder toward realistic biological membrane simulations. J Comput Chem. 2014;35:1997–2004.
   PubMed Web of Science ®Google Scholar
• Huang J, Rauscher S, Nawrocki G, et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017;14:71–73.
   PubMed Web of Science ®Google Scholar
• Klauda JB, Venable RM, Freites JA, et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B. 2010;114:7830–7843.
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe K, Hatcher E, Acharya C, et al. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2009;31:671–690.
   Web of Science ®Google Scholar
• Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935.
   Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald: an N · log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
   Web of Science ®Google Scholar
• Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341.
   Web of Science ®Google Scholar
• Miyamoto S, Kollman PA. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem. 1992;13:952–962.
   Web of Science ®Google Scholar
• Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802.
   PubMed Web of Science ®Google Scholar
• Case DA, Ben-Shalom IY, Brozell SR, et al. AMBER 2018. San Francisco: University of California; 2018.
   Google Scholar
• Salomon-Ferrer R, Götz AW, Poole D, et al. Routine microsecond molecular dynamics simulations with AMBER – Part II: particle Mesh Ewald. J Chem Theory Comput. 2013;9:3878–3888.
   PubMed Web of Science ®Google Scholar
• Götz AW, Williamson MJ, Xu D, et al. Routine microsecond molecular dynamics simulations with AMBER – Part I: generalized born. J Chem Theory Comput. 2012;8:1542–1555.
   PubMed Web of Science ®Google Scholar
• Le Grand S, Götz AW, Walker RC. SPFP: speed without compromise—a mixed precision model for GPU accelerated molecular dynamics simulations. Comp Phys Comm. 2013;184:374–380.
   Web of Science ®Google Scholar
• Pastor RW, Brooks BR, Szabo A. An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol Phys. 1988;65:1409–1419.
   Web of Science ®Google Scholar
• Loncharich RJ, Brooks BR, Pastor RW. Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-actylananyl-N’-methylamide. Biopolymers. 1992;32:523–535.
   PubMed Web of Science ®Google Scholar
• Bernardi R, Bhandarkar M, Bhatele A, et al. NAMD user’s guide version 2.13 November 9, 2018.
   Google Scholar
• Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. J Chem Phys. 1994;101:4177–4189.
   Web of Science ®Google Scholar
• Feller SE, Zhang Y, Pastor RW, et al. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys. 1995;103:4613–4621.
   Web of Science ®Google Scholar
• Chen LY. Hybrid steered molecular dynamics approach to computing absolute binding free energy of ligand-protein complexes: a brute force approach that is fast and accurate. J Chem Theory Comput. 2015;11:1928–1938.
   PubMed Web of Science ®Google Scholar
• Villarreal OD, Yu LL, Rodriguez RA, et al. Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. Biochem Biophys Res Commun. 2017;483:203–208.
   PubMed Web of Science ®Google Scholar
• Chen LY. Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach. Mol Membr Biol. 2015;32:19–25.
   PubMed Web of Science ®Google Scholar
• Yu LL, Rodriguez RA, Chen LL, et al. 1,3-propanediol binds deep inside the channel to inhibit water permeation through aquaporins. Protein Sci. 2016;25:433–441.
   PubMed Web of Science ®Google Scholar
• Rodriguez RA, Yu LL, Chen LY. Computing protein-protein association affinity with hybrid steered molecular dynamics. J Chem Theory Comput. 2015;11:4427–4438.
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–38.
   PubMed Web of Science ®Google Scholar
• Maciver B, Smith CP, Hill WG, et al. Functional characterization of mouse urea transporters UT-A2 and UT-A3 expressed in purified Xenopus laevis oocyte plas- ma membranes. Am J Physiol Renal Physiol. 2008;294:F956–F964.
   PubMed Web of Science ®Google Scholar
• Mannuzzu LM, Moronne MM, Macey RI. Estimate of the number of urea transport sites in erythrocyte ghosts using a hydrophobic mercurial. J Membr Biol. 1993;133:85–97.
   PubMed Web of Science ®Google Scholar
• Rousselet G, Ripoche P, Bailly P. Tandem sequence repeats in urea transporters: identification of an urea transporter signature sequence. Am J Physiol. 1996;270:F554–F555.
   PubMedGoogle Scholar
• Müller EM, Hub JS, Grubmüller H, et al. Is TEA an inhibitor for human aquaporin-1? Pflugers Arch. 2008;456:663–669.
   PubMed Web of Science ®Google Scholar