Exploration of Na+,K+-ATPase ion permeation pathways via molecular dynamic simulation and electrostatic analysis
- 70 Downloads
- 1 Citations
Abstract
Biologically-inspired nanodevices can serve as “natural” alternatives to conventional semiconductor devices in many applications from information storage to mechanical rotors. In this work we consider an ATP-powered transmembrane protein, the Na+,K+-ATPase, which has appealing functionality but still lacks an “atomistic” picture capable of elucidating its operation. The vast collection of experimental literature on the Na+,K+-ATPase gives a unique advantage to this protein in developing and validating computational tools. We have performed extensive molecular dynamic simulations of the Na+,K+-ATPase in an accurate biological environment, followed by time-averaged electrostatic analysis, to investigate the ion-binding loci and access/egress pathways that cations may take through the protein as they are transported across the membrane.
Keywords
Na+,K+-ATPase Bionano Homology modeling Electrostatics Molecular dynamicsPreview
Unable to display preview. Download preview PDF.
References
- 1.Asenov, A., et al.: IEEE Trans. Electron Devices 50, 1837 (2003) CrossRefGoogle Scholar
- 2.Niemeyer, C.M., Mirkin, C.A.: Nanobiotechnology: Concepts, Applications and Perspectives. Wiley-VCH, Weinheim (2004) Google Scholar
- 3.van den Heuvel, M., Dekker, C.: Science 317, 333 (2007) CrossRefGoogle Scholar
- 4.Saraniti, M., et al.: J. Comp. Elec. 5, 405 (2006) CrossRefGoogle Scholar
- 5.Toyoshima, C., et al.: Nature 432, 361 (2004) CrossRefGoogle Scholar
- 6.Apell, H.J.: Bioelectrochemistry 63, 149 (2004) CrossRefGoogle Scholar
- 7.Horisberger, J.D.: Physiology (Bethesda) 19, 377 (2004) Google Scholar
- 8.Law, R.J., et al.: J. Mol. Graph. Model 24, 157 (2005) CrossRefGoogle Scholar
- 9.Laskowski, R.A., et al.: J. Appl. Cryst. 26, 283 (1993) CrossRefGoogle Scholar
- 10.Morth, J.P., et al.: Nature 450, 1043 (2007) CrossRefGoogle Scholar
- 11.Sweadner, K.J., Donnet, C.: Biochem. J. 356, 685 (2001) Google Scholar
- 12.Toyoshima, C., et al.: Nature 405, 647 (2000) CrossRefGoogle Scholar
- 13.Munson, K., et al.: Biochemistry 44, 5267 (2005) CrossRefMathSciNetGoogle Scholar
- 14.Einholm, A.P., et al.: J. Biol. Chem. 282, 23854 (2007) CrossRefGoogle Scholar
- 15.Marti-Renom, M.A., et al.: Ann. Rev. Biophys. Biomol. Str. 29, 291 (2000) CrossRefGoogle Scholar
- 16.Kandt, C., et al.: Methods 41, 475 (2007) CrossRefGoogle Scholar
- 17.Fonseca, J.E., et al.: Nanotechnology 18, 424022 (2007) CrossRefGoogle Scholar
- 18.Humphrey, W., et al.: J. Mol. Graph. 14, 33 (1996) CrossRefGoogle Scholar
- 19.Aksimentiev, A., Schulten, K.: Biophys. J. 88, 3745 (2005) CrossRefGoogle Scholar
- 20.Li, C., et al.: P. Nat. Ac. Sci. 102, 12706 (2005) CrossRefGoogle Scholar
- 21.Schneider, H., Scheiner-Bobis, G.: J. Biol. Chem. 272, 16158 (1997) CrossRefGoogle Scholar
- 22.Capendeguy, O., Horisberger, J.D.: J. Physiol. 565, 207 (2005) CrossRefGoogle Scholar
- 23.Capendeguy, O., et al.: J. Gen. Physiol. 127, 341 (2006) CrossRefGoogle Scholar