Structure, dynamics, and ion conductance of the phospholamban pentamer

Biophysical Journal

Volumn 96, Issue 12, 2009, Pages 4853-4865

  Maffeo, Christopher ^a   Aksimentiev, Aleksei ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ION; ION CHANNEL; PHOSPHOLAMBAN;

ARTICLE; ATOM; BELLFLOWER; CYTOPLASM; FEASIBILITY STUDY; FLOWER; FLUCTUATING ASYMMETRY; FLUORESCENCE RESONANCE ENERGY TRANSFER; ION CONDUCTANCE; LIPID BILAYER; MEMBRANE POTENTIAL; MICELLE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE;

EID: 68949090107     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.03.053     Document Type: Article

References (45)

1. Wegener, A. D., H. K. Simmerman, J. P. Lindemann, and L. R. Jones. 1989. Phospholamban phosphorylation in intact ventricles: Phosphorylation of serine 16 and threonine 17 in response to beta-adrenergic stimulation. J. Biol. Chem. 264:11468-11474.
2. 2+-ATPase-phospholamban interaction and dilated cardiomyopathy. Biochem. Biophys. Res. Commun. 322:1214-1222.
3. 2+ pump of cardiac sarcoplasmic reticulum. J. Biol. Chem. 275:41487-41494.
4. 2+-selective channels in lipid bilayers. J. Biol. Chem. 263:18364-18368.
5. - channel from human atrial myocytes: involvement of phospholamban. J. Mol. Cell. Cardiol. 28:767-780.
6. MacLennan, D. H., and E. G. Kranias. 2003. Phospholamban: a crucial regulator of cardiac contractility. Nat. Rev. Mol. Cell Biol. 4:566-577.
7. 15N heteronuclear NMR spectroscopy shows four dynamic domains for phospholamaban reconstituted in dodecylphosphocholine micelles. Biophys. J. 87:1205-1214.
8. 2+ ATPase. Proc. Natl. Acad. Sci. USA. 100:467-472.
9. 2+-ATPase. Biochem. Biophys. Res. Commun. 369:188-194.
10. Houndonougbo, Y., K. Kuczera, and G. S. Jas. 2005. Structure and dynamics of phospholamban in solution and in membrane bilayer: computer simulations. Biochemistry. 44:1780-1792.
11. Paterlini, M. G., and D. D. Thomas. 2005. The α-helical propensity of the cytoplasmic domain of phospholamban: a molecular dynamics simulation of the effect of phosphorylation and mutation. Biophys. J. 88:3243-3251.
12. Sugita, Y., N. Miyashita, T. Yoda, M. Ikeguchi, and C. Toyoshima. 2006. Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study. Biochemistry. 45:11752-11761.
13. Pantano, S., and E. Carafoli. 2007. The role of phosphorylation on the structure and dynamics of phospholamban: a model from molecular simulations. Proteins. 66:930-940.
14. Zamoon, J., A. M. and David D. Thomas, and G. Veglia. 2003. NMR solution structure and topological orientation of monomeric phospholamban in dodecylphosphocholine micelles. Biophys. J. 85:2589-2598.
15. Metcalfe, E., N. Traaseth, and G. Veglia. 2005. Serine 16 phosphorylation induces an order-to-disorder transition in monomeric phospholamban. Biochemistry. 44:4386-4396.
16. Adams, P. D., I. T. Arkin, D. M. Engelman, and A. T. Brunger. 1995. Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Nat. Struct. Mol. Biol. 2:154-162.
17. Sansom, M. S. P., G. R. Smith, O. S. Smart, and S. O. Smith. 1997. Channels formed by the transmembrane helix of phospholamban: a simulation study. Biophys. Chem. 69:269-281.
18. Oxenoid, K., and J. J. Chou. 2005. The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc. Natl. Acad. Sci. USA. 102:10870-10875.
19. Robia, S. L., N. C. Flohr, and D. D. Thomas. 2005. Phospholamban pentamer quaternary conformation determined by in-gel fluorescence anisotropy. Biochemistry. 44:4302-4311.
20. Nesmelov, Y., C. Karim, L. Song, P. Fajer, and D. Thomas. 2007. Rotational dynamics of phospholamban determined by multifrequency electron paramagnetic resonance. Biophys. J. 93:2805-2812.
21. Traaseth, N. J., R. Verardi, K. D. Torgersen, C. B. Karim, D. D.Thomas, et al. 2007.Spectroscopic validation of the pentameric structure of phospholamban. Proc. Natl. Acad. Sci. USA. 104:14676-14681.
22. Phillips, J. C., R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, et al. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802.
23. MacKerell, Jr., A., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. Evanseck, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
24. MacKerrel, A. D., M. Feig, and C. L. Brooks III. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.
25. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Oxford University Press, New York.
26. Martyna, G. J., D. J. Tobias, and M. L. Klein. 1994. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101:4177-4189.
27. Batcho, P. F., D. A. Case, and T. Schlick. 2001. Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. J. Chem. Phys. 115:4003-4018.
28. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
29. Marrink, S. J., A. H. de Vries, and A. E. Mark. 2004. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B. 108: 750-760.
30. Marrink, S. J., and A. E. Mark. 2003. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. J. Am. Chem. Soc. 125:15233-15242.
31. Shih, A. Y., A. Arkhipov, P. L. Freddolino, and K. Schulten. 2006. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B. 110:3674-3684.
32. Marrink, S. J., H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries. 2007. The MARTINI forcefield: coarse grained model for biomolecular simulations. J. Phys. Chem. B. 111:7812-7824.
33. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14:33-38.
34. Lauterwein, J., C. Bosch, L. Brown, and K. Wuthrich. 1979. Physicochemical studies of the protein-lipid interactions in melittin-containing micelles. Biochim. Biophys. Acta. 556:244-264.
35. Anishkin, A., and S. Sukharev. 2004. Water dynamics and dewetting transitions in the small mechanosensitive channel MscS. Biophys. J. 86:2883-2895.
36. Gullingsrud, J., R. Braun, and K. Schulten. 1999. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J. Comput. Phys. 151:190-211.
37. Smart, O. S., J. G. Neduvelil, X. Wang, B. A. Wallace, and M. S. P. Sansom. 1996. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14:354-360.
38. Gullingsrud, J., and K. Schulten. 2004. Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophys. J. 86:3496-3509.
39. Liu, Y., and J. F. Nagle. 2004. Diffuse scattering provides material parameters and electron density profiles of biomembranes. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 69:040901.
40. Aksimentiev, A., and K. Schulten. 2005. Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability and the electrostatic potential map. Biophys. J. 88:3745-3761.
41. Anishkin, A., B. Akitake, and S. Sukharev. 2008. Characterization of the resting MscS: modeling and analysis of the closed bacterial mechanosensitive channel of small conductance. Biophys. J. 94:1252-1266.
42. Isralewitz, B., S. Izrailev, and K. Schulten. 1997. Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations. Biophys. J. 73:2972-2979.
43. Kim, T., J. Lee, and W. Im. 2009. Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes. Proteins. 76:86-88.
44. Park, S., and S. Opella. 2005. Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch. J. Mol. Biol. 350:310-318.
45. Yeagle, P., M. Bennett, V. Lemaître, and A. Watts. 2007. Transmembrane helices of membrane proteins may flex to satisfy hydrophobic mismatch. Biochimica et Biophysica Acta. 1768:530-537.