Liquid but durable: Molecular dynamics simulations explain the unique properties of archaeal-like membranes

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Chugunov, Anton O ^a   Volynsky, Pavel E ^a   Krylov, Nikolay A ^a,b   Boldyrev, Ivan A ^a   Efremov, Roman G ^a,c,d  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

^c MOSCOW INSTITUTE OF PHYSICS AND TECHNOLOGY   (Russian Federation)

^d NATIONAL RESEARCH UNIVERSITY HIGHER SCHOOL OF ECONOMICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL MEMBRANE; LIPID BILAYER; MEMBRANE LIPID; WATER;

ARCHAEON; ARTIFICIAL MEMBRANE; BIOPHYSICS; CELL MEMBRANE; CHEMISTRY; LIPID BILAYER; METABOLISM; MOLECULAR DYNAMICS;

ARCHAEA; BIOPHYSICAL PHENOMENA; CELL MEMBRANE; LIPID BILAYERS; MEMBRANE LIPIDS; MEMBRANES, ARTIFICIAL; MOLECULAR DYNAMICS SIMULATION; WATER;

EID: 84948460072     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep07462     Document Type: Article

References (32)

1. Offre, P., Spang, A. & Schleper, C. Archaea in biogeochemical cycles. Annu Rev Microbiol 67, 437-57 (2013).
2. Goldenfeld, N. Looking in the right direction: Carl Woese and evolutionary biology. RNA Biol 11 (2014).
3. Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87, 4576-9 (1990).
4. Koga, Y. From promiscuity to the lipid divide: on the evolution of distinct membranes in Archaea and Bacteria. J Mol Evol 78, 234-42 (2014).
5. Oger, P. M. & Cario, A. Adaptation of the membrane in Archaea. Biophys Chem 183, 42-56 (2013).
6. Lombard, J., Lopez-Garcia, P. & Moreira, D. Phylogenomic investigation of phospholipid synthesis in archaea. Archaea 2012, 630910 (2012).
7. Chong, P. L., Ayesa, U., Daswani, V. P. & Hur, E. C. On physical properties of tetraether lipid membranes: effects of cyclopentane rings. Archaea 2012, 138439 (2012).
8. Chong, P. L., Sulc, M. & Winter, R. Compressibilities and volume fluctuations of archaeal tetraether liposomes. Biophys J 99, 3319-26 (2010).
9. Bartucci, R., Gambacorta, A., Gliozzi, A., Marsh, D. & Sportelli, L. Bipolar tetraether lipids: chain flexibility and membrane polarity gradients from spinlabel electron spin resonance. Biochemistry 44, 15017-23 (2005).
10. Chong, P. L., Ravindra, R., Khurana, M., English, V. & Winter, R. Pressure perturbation and differential scanning calorimetric studies of bipolar tetraether liposomes derived from the thermoacidophilic archaeon Sulfolobus acidocaldarius. Biophys J 89, 1841-9 (2005).
11. Elferink, M. G., deWit, J. G., Driessen, A. J. & Konings, W. N. Stability and protonpermeability of liposomes composed of archaeal tetraether lipids. Biochim Biophys Acta 1193, 247-54 (1994).
12. Dante, S. et al. Thermal Stability of Bipolar Lipid Langmuir Blodgett Films by XRay Diffraction. Mol Cryst Liq Crys A 262, 191-207 (1995).
13. Chong, P. L. Archaebacterial bipolar tetraether lipids: Physico-chemical and membrane properties. Chem Phys Lipids 163, 253-65 (2010).
14. Boyd, E. S., Hamilton, T. L., Wang, J., He, L. & Zhang, C. L. The role of tetraether lipid composition in the adaptation of thermophilic archaea to acidity. Front Microbiol 4, 62 (2013).
15. Zhai, Y. et al. Physical properties of archaeal tetraether lipid membranes as revealed by differential scanning and pressure perturbation calorimetry, molecular acoustics, and neutron reflectometry: effects of pressure and cell growth temperature. Langmuir 28, 5211-7 (2012).
16. Nishihara, M. & Koga, Y. Extraction and composition of polar lipids from the archaebacterium, Methanobacterium thermoautotrophicum: effective extraction of tetraether lipids by an acidified solvent. J Biochem 101, 997-1005 (1987).
17. Dannenmuller, O. et al. Membrane properties of archaeal macrocyclic diether phospholipids. Chemistry 6, 645-54 (2000).
18. Stewart, L. C., Kates, M., Ekiel, I. H. & Smith, I. C. P. Molecular order and dynamics of diphytanylglycerol phospholipids: a 2H and 31P-NMR study. Chem Phys Lipids 54, 115-129 (1990).
19. Benvegnu, T., Lemiègre, L. & Cammas-Marion, S. Archaeal Lipids: Innovative Materials for Biotechnological Applications. Eur J Org Chem 2008, 4725-4744 (2008).
20. Bulacu, M., Periole, X. & Marrink, S. J. In silico design of robust bolalipid membranes. Biomacromolecules 13, 196-205 (2012).
21. Gabriel, J. L. & Chong, P. L. Molecular modeling of archaebacterial bipolar tetraether lipid membranes. Chem Phys Lipids 105, 193-200 (2000).
22. Shinoda, W., Shinoda, K., Baba, T. & Mikami, M. Molecular dynamics study of bipolar tetraether lipid membranes. Biophys J 89, 3195-202 (2005).
23. Polyansky, A. A., Volynsky, P. E., Arseniev, A. S. & Efremov, R. G. Adaptation of a membrane-active peptide to heterogeneous environment. II. The role of mosaic nature of the membrane surface. J Phys Chem B 113, 1120-6 (2009).
24. Pyrkova, D. V. et al. Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact. J Biomol Struct Dyn 31, 87-95 (2013).
25. Volynsky, P. E., Polyansky, A. A., Simakov, N. A., Arseniev, A. S. & Efremov, R. G. Effect of lipid composition on the ''membrane response'' induced by a fusion peptide. Biochemistry 44, 14626-37 (2005).
26. Krylov, N. A., Pentkovsky, V. M. & Efremov, R. G. Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations. ACS Nano 7, 9428-42 (2013).
27. Franck, J. M., Scott, J. A. & Han, S. Nonlinear scaling of surface water diffusion with bulk water viscosity of crowded solutions. J Am Chem Soc 135, 4175-8 (2013).
28. Pyrkova, D. V., Tarasova, N. K., Pyrkov, T. V., Krylov, N. A. & Efremov, R. G. Atomic-scale lateral heterogeneity and dynamics of two-component lipid bilayers composed of saturated and unsaturated phosphatidylcholines. Soft Matter 7, 2569 (2011).
29. Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E.GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4, 435-447 (2008).
30. Jambeck, J. P. & Lyubartsev, A. P. Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J Phys Chem B 116, 3164-79 (2012).
31. Jämbeck, J. P. M. & Lyubartsev, A. P. An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. J Chem Theory Comput 8, 2938-2948 (2012).
32. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J Chem Phys 79, 926 (1983).