Molecular dynamics simulation of the transmembrane subunit of BtuCD in the lipid bilayer

Science China Life Sciences

Volumn 53, Issue 5, 2010, Pages 620-630

  Sun, Ting Guang ^a,b   Liu, Ming ^a   Chen, Wei Zu ^a   Wang, Cun Xin ^a  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^b GUANGXI UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

BtuCD; Functional motion; POPC; Principal component analysis

Indexed keywords

ABC TRANSPORTER; BTUC PEPTIDE, E COLI; CYANOCOBALAMIN; ESCHERICHIA COLI PROTEIN; LIPID BILAYER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; LIPID BILAYER; METABOLISM; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS;

ATP-BINDING CASSETTE TRANSPORTERS; ESCHERICHIA COLI PROTEINS; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; VITAMIN B 12;

ESCHERICHIA COLI;

EID: 77953699035     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-010-0103-7     Document Type: Article

References (44)

1. Schneider E, Hunke S. ATP-binding-cassette (ABC) transport systems: Functional and structural aspects of the ATP-hydrolyzing subunits/domains. Fems Microbiol Rev, 1998, 22: 1-20.
2. Abele R, Tampe R. Function of the transport complex TAP in cellular immune recognition. Biochim Biophys Acta-Biomembr, 1999, 1461: 405-419.
3. Akabas M H. Cystic fibrosis transmembrane conductance regulator-structure and function of an epithelial chloride channel. J Biol Chem, 2000, 275: 3729-3732.
4. Ehrmann M, Ehrle R, Hofmann E, et al. The ABC maltose transporter. Mol Microbiol, 1998, 29: 685-694.
5. Doerrler W T, Raetz C R H. ATPase activity of the MsbA lipid flippase of Escherichia coli. J Biol Chem, 2002, 277: 36697-36705.
6. van Veen H W, Margolles A, Muller M, et al. The homodimeric ATP-binding cassette transporter LmrA mediates multidrug transport by an alternating two-site (two-cylinder engine) mechanism. Embo J, 2000, 19: 2503-2514.
7. Gottesman M M, Fojo T, Bates S E. Multidrug resistance in cancer: Role of ATP-dependent transporters. Nat Rev Cancer, 2002, 2: 48-58.
8. Chen J M, Cutler C, Jacques C, et al. A combined analysis of the cystic fibrosis transmembrane conductance regulator: Implications for structure and disease models. Mol Biol Evol, 2001, 18: 1771-1788.
9. Higgins C F. ABC transporters: Physiology, structure and mechanism-an overview. Res Microbiol, 2001, 152: 205-210.
10. Jones P M, George A M. Subunit interactions in ABC transporters: Towards a functional architecture. FEMS Microbiol Lett, 1999, 179: 187-202.
11. Reyes C L, Chang G. Structure of the ABC transporter MsbA in complex with ADP-vanadate and lipopolysaccharide. Science, 2005, 308: 1028-1031.
12. Dawson R J P, Locher K P. Structure of a bacterial multidrug ABC transporter. Nature, 2006, 443: 180-185.
13. Locher K P, Lee A T, Rees D C. The E-coli BtuCD structure: A framework for ABC transporter architecture and mechanism. Science, 2002, 296: 1091-1098.
14. Karpowich N K, Huang H H, Smith P C, et al. Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon substrate binding. J Biol Chem, 2003, 278: 8429-8434.
15. Davidson A L, Chen J. ATP-binding cassette transporters in bacteria. Annu Rev Biochem, 2004, 73: 241-268.
16. Ash W L, Zlomislic M R, Oloo E O, et al. Computer simulations of membrane proteins. Biochim Biophys Acta-Biomembr, 2004, 1666: 158-189.
17. Roux B, Schulten K. Computational studies of membrane channels. Structure, 2004, 12: 1343-1351.
18. Oloo E O, Tieleman D P. Conformational transitions induced by the binding of MgATP to the vitamin B-12 ATP-binding cassette (ABC) transporter BtuCD. J Biol Chem, 2004, 279: 45013-45019.
19. Tanizaki S, Feig M. Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. J Phys Chem B, 2006, 110: 548-556.
20. Ivetac A, Campbell J D, Sansom M S P. Dynamics and function in a bacterial ABC transporter: Simulation studies of the BtuCDF system and its components. Biochemistry, 2007, 46: 2767-2778.
21. Kundu S, Jernigan R L. Molecular mechanism of domain swapping in proteins: An analysis of slower motions. Biophys J, 2004, 86: 3846-3854.
22. Wang Y M, Rader A J, Bahar I, et al. Global ribosome motions revealed with elastic network model. J Struct Biol, 2004, 147: 302-314.
23. Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys, 1983, 79: 926-935.
24. Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph, 1996, 14: 33-38.
25. llips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem, 2005, 26: 1781-1802.
26. MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B, 1998, 102: 3586-3616.
27. York D M, Darden T A, Pedersen L G. The effect of long-range electrostatic interactions in simulations of macromolecular crystals- a comparison of the ewald and truncated list methods. J Chem Phys, 1993, 99: 8345-8348.
28. Amadei A, Linssen A B M, Berendsen H J C. Essential dynamics of proteins. Proteins, 1993, 17: 412-425.
29. Lindahl E, Hess B, van der Spoel D. GROMACS 3. 0: A package for molecular simulation and trajectory analysis. J Mol Model, 2001, 7: 306-317.
30. Pasenkiewicz-Gierula M, Murzyn K, Rog T, et al. Molecular dynamics simulation studies of lipid bilayer systems. Acta Biochim Pol, 2000, 47: 601-611.
31. Pandit S A, Chiu S W, Jakobsson E, et al. Cholesterol surrogates: A comparison of cholesterol and 16: 0 ceramide in POPC Bilayers. Biophys J, 2007, 92: 920-927.
32. Smaby J M, Momsen M M, Brockman H L, et al. Phosphatidylcholine acyl unsaturation modulates the decrease in interfacial elasticity induced by cholesterol. Biophys J, 1996, 73: 1492-1505.
33. Hyslop P A, Morel B, Sauerheber R D. Organization and interaction of cholesterol and phosphatidylcholine in model bilayer-membranes. Biochemistry, 1990, 29: 1025-1038.
34. Patra M, Salonen E, Terama E, et al. Under the influence of alcohol: the effect of ethanol and methanol on lipid bilayers. Biophys J, 2006, 90: 1121-1135.
35. Rand R P, Parsegian V A. Hydration forces between phospholipid-bilayers. Biochimica Et Biophysica Acta, 1989, 988: 351-376.
36. Gullingsrud J, Schulten K. Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophys J, 2004, 86: 3496-3509.
37. Hvorup R N, Goetz B A, Niederer M, et al. Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF. Science, 2007, 317: 1387-1390.
38. Ambudkar S V, Cardarelli C O, Pashinsky I, et al. Relation between the turnover number for vinblastine transport and for vinblastine-stimulated ATP hydrolysis by human P-glycoprotein. J Biol Chem, 1997, 272: 21160-21166.
39. Haider S, Grottesi A, Hall B A, et al. Conformational dynamics of the substrate-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: Toward an understanding of Kir channel gating. Biophys J, 2005, 88: 3310-3320.
40. Grottesi A, Domene C, Hall B, et al. Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations. Biochemistry, 2005, 44: 14586-14594.
41. Cadieux N, Bradbeer C, Reeger-Schneider E, et al. Identification of the periplasmic cobalamin-binding protein BtuF of Escherichia coli. J Bacteriol, 2002, 184: 706-717.
42. Kandt C, Xu Z T, Tieleman D P. Opening and closing motions in the periplasmic vitamin B-12 binding protein BtuF. Biochemistry, 2006, 45: 13284-13292.
43. Hollenstein K, Frei D C, Locher K P. Structure of an ABC transporter in complex with its binding protein. Nature, 2007, 446: 213-216.
44. Dawson R J P, Hollenstein K, Locher K P. Uptake or extrusion: Crystal structures of full ABC transporters suggest a common mechanism. Mol Microbiol, 2007, 65: 250-257.