Dynamics of lipids, cholesterol, and transmembrane α-helices from microsecond molecular dynamics simulations

Journal of Physical Chemistry B

Volumn 118, Issue 47, 2014, Pages 13590-13600

  Baker, Michelle K ^a   Abrams, Cameron F ^a  

^a Drexel University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BROWNIAN MOVEMENT; CHOLESTEROL; COMPUTER SIMULATION; MOLECULAR DYNAMICS; PEPTIDES;

CONFIGURATIONAL SPACES; DIPALMITOYL PHOSPHATIDYLCHOLINE; MEMBRANE THICKNESS; MODEL MEMBRANES; MOLECULAR DYNAMICS SIMULATIONS; PEPTIDE SEQUENCES; TEMPERATURE DIFFERENCES; TRANS-MEMBRANE PROTEINS;

DIFFUSION;

CHOLESTEROL; DIPALMITOYLPHOSPHATIDYLCHOLINE; GLYCOPROTEIN GP 41; GP41 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; LIPID; LIPID BILAYER; WATER;

CHEMISTRY; DIFFUSION; LIPID BILAYER; MOLECULAR DYNAMICS; PROTEIN SECONDARY STRUCTURE; TEMPERATURE;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; CHOLESTEROL; DIFFUSION; HIV ENVELOPE PROTEIN GP41; LIPID BILAYERS; LIPIDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, SECONDARY; TEMPERATURE; WATER;

EID: 84914118608     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp507027t     Document Type: Article

References (42)

1. Guyader, M.; Kiyokawa, E.; Abrami, L.; Turelli, P.; Trono, D. Role for Human Immunodeficiency Virus Type 1 Membrane Cholesterol in Viral Internalization J. Virol. 2002, 76, 10356-10364
2. Waheed, A. A.; Freed, E. O. Lipids and Membrane Microdomains in HIV-1 Replication Virus Res. 2009, 143, 162-176
3. Wohlert, J.; Edholm, O. Dynamics in Atomistic Simulations of Phospholipid Membranes: Nuclear Magnetic Resonance Relaxation Rates and Lateral Diffusion J. Chem. Phys. 2006, 125, 204703-1-204703-10
4. Sanderson, J. M. Resolving the Kinetics of Lipid, Protein and Peptide Diffusion in Membranes Mol. Membr. Biol. 2012, 29, 118-143
5. Falck, E.; Róg, T.; Karttunen, M.; Vattulainen, I. Lateral Diffusion in Lipid Membranes through Collective Flows J. Am. Chem. Soc. 2008, 130, 44-45
6. Niemelä, P. S.; Miettinen, M. S.; Monticelli, L.; Hammaren, H.; Bjelkmar, P.; Murtola, T.; Lindahl, E.; Vattulainen, I. Membrane Proteins Diffuse as Dynamic Complexes with Lipids J. Am. Chem. Soc. 2010, 132, 7574-7575
7. Lindahl, E.; Edholm, O. Molecular Dynamics Simulation of NMR Relaxation Rates and Slow Dynamics in Lipid Bilayers J. Chem. Phys. 2001, 115, 4938-4950
8. Roark, M.; Feller, S. E. Molecular Dynamics Simulation Study of Correlated Motions in Phospholipid Bilayer Membranes J. Phys. Chem. B 2009, 113, 13229-13234
9. Andoh, Y.; Okazaki, S.; Ueoka, R. Molecular Dynamics Study of Lipid Bilayers Modeling the Plasma Membranes of Normal Murine Thymocytes and Leukemic GRSL Cells Biochim. Biophys. Acta 2013, 1828, 1259-1270
10. Jeon, J.-H.; Monne, H. M.-S.; Javanainen, M.; Metzler, R. Anomalous Diffusion of Phospholipids and Cholesterols in a Lipid Bilayer and Its Origins Phys. Rev. Lett. 2012, 109, 188103-1-188103-5
11. Falck, E.; Patra, M.; Karttunen, M.; Hyvönen, M. T.; Vattulainen, I. Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers Biophys. J. 2004, 87, 1076-1091
12. Shaw, D. E.; Deneroff, M. M.; Dror, R.; Kuskin, J. S.; Larson, R. H.; Salmon, J. K.; Young, C.; Batson, B.; Bowers, K. J.; Chao, J. C. Anton, a Special-Purpose Machine for Molecular Dynamics Simulation Commun. ACM 2008, 91-97
13. Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Long-Timescale Molecular Dynamics Simulations of Protein Structure and Function Curr. Opin. Struct. Biol. 2009, 19, 120-127
14. Gangupomu, V. K.; Abrams, C. F. All-Atom Models of the Membrane-Spanning Domain of HIV-1 gp41 from Metadynamics Biophys. J. 2010, 99, 3438-3444
15. Baker, M. K.; Gangupomu, V. K.; Abrams, C. F. Characterization of the Water Defect at the HIV-1 gp41 Membrane Spanning Domain in Bilayers With and Without Cholesterol using Molecular Simulations Biochim. Biophys. Acta 2014, 694, 26-31
16. Jo, S.; Lim, J. B.; Klauda, J. B.; Im, W. CHARMM-GUI Membrane Builder for Mixed Bilayers and its Application to Yeast Membranes Biophys. J. 2009, 97, 50-58
17. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
18. Mackerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
19. Feller, S. E.; MacKerell, A. D. An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids J. Phys. Chem. B 2000, 104, 7510-7515
20. Klauda, J. B.; Venable, R. M.; Freites, J. A.; OConnor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D.; Pastor, R. W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types J. Phys. Chem. B 2010, 114, 7830-7843
21. Pastor, R. W.; MacKerell, A. D. Development of the CHARMM Force Field for Lipids J. Phys. Chem. Lett. 2011, 2, 1526-1532
22. Shan, Y.; Klepeis, J. L.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation J. Chem. Phys. 2005, 122, 054101-1-054101-13
23. Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms J. Chem. Phys. 1994, 101, 4177-4189
24. Lippert, R. A.; Predescu, C.; Ierardi, D. J.; Mackenzie, K. M.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Accurate and Efficient Integration for Molecular Dynamics Simulations at Constant Temperature and Pressure J. Chem. Phys. 2013, 139, 164106-1-164106-11
25. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 27-28, 33-38
26. Basconi, J. E.; Shirts, M. R. Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations J. Chem. Theory Comput. 2013, 9, 2887-2899
27. Harvey, S. C.; Tan, R. K.-Z.; Cheatham, T. E. The Flying Ice Cube: Velocity Rescaling in Molecular Dynamics Leads to Violation of Energy Equipartition J. Comput. Chem. 1998, 19, 726-740
28. Chiu, S.-W.; Clark, M.; Subramaniam, S.; Jakobsson, E. Collective Motion Artifacts Arising in Long-Duration Molecular Dynamics Simulations J. Comput. Chem. 2000, 21, 121-131
29. 2H NMR Experiments Eur. Biophys. J. 2007, 36, 919-931
30. Levine, B. G.; Stone, J. E.; Kohlmeyer, A. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units: Radial Distribution Function Histogramming J. Comput. Phys. 2011, 230, 3556-3569
31. Cournia, Z.; Ullmann, G. M.; Smith, J. C. Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine Membrane: A Molecular Dynamics Simulation Study J. Phys. Chem. B 2007, 111, 1786-1801
32. Klauda, J. B.; Brooks, B. R.; Pastor, R. W. Dynamical Motions of Lipids and a Finite Size Effect in Simulations of Bilayers J. Chem. Phys. 2006, 125, 144710-1-144710-8
33. 1H Pulsed Field Gradient Magic Angle Spinning NMR Biophys. J. 2005, 89, 2504-2512
34. Filippov, A. V.; Rudakova, M. A.; Oradd, G.; Lindblom, G. Lateral Diffusion of Saturated Phosphatidylcholines in Cholesterol-Containing Bilayers Biophyzika 2007, 52, 476-485
35. Scherfeld, D.; Kahya, N.; Schwille, P. Lipid Dynamics and Domain Formation in Model Membranes Composed of Ternary Mixtures of Unsaturated and Saturated Phosphatidylcholines and Cholesterol Biophys. J. 2003, 85, 3758-3768
36. Braun, A. R.; Brandt, E. G.; Edholm, O.; Nagle, J. F.; Sachs, J. N. Determination of Electron Density Profiles and Area From Simulations of Undulating Membranes Biophys. J. 2011, 100, 2112-2120
37. Apajalahti, T.; Niemelä, P.; Govindan, P. N.; Miettinen, M. S.; Salonen, E.; Marrink, S.-J.; Vattulainen, I. Concerted Diffusion of Lipids in Raft-Like Membranes Faraday Discuss. 2010, 144, 411-430
38. Jo, S.; Rui, H.; Lim, J. B.; Klauda, J. B.; Im, W. Cholesterol Flip-Flop: Insights From Free Energy Simulation Studies J. Phys. Chem. B 2010, 114, 13342-13348
39. Choubey, A.; Kalia, R.; Malmstadt, N.; Nakano, A.; Vashishta, P. Cholesterol Translocation in a Phospholipid Membrane Biophys. J. 2013, 104, 2429-2436
40. Bennett, W. F. D.; MacCallum, J. L.; Hinner, M. J.; Marrink, S. J.; Tieleman, D. P. Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments J. Am. Chem. Soc. 2009, 131, 12714-12720
41. Lim, J. B.; Rogaski, B.; Klauda, J. B. Update of the Cholesterol Force Field Parameters in CHARMM J. Phys. Chem. B 2012, 116, 203-210
42. Neale, C.; Hsu, J. C. Y.; Yip, C. M.; Pomès, R. Indolicidin Binding Induces Thinning of a Lipid Bilayer Biophys. J. 2014, 106, L29-L31