The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
Lipids Out of Equilibrium: Energetics of Desorption and Pore Mediated Flip-Flop
Open accessAbstract
The potential of mean force (PMF) of a phospholipid in a bilayer is a key thermodynamic property that describes the energetic cost of localized lipid defects. We have calculated the PMF by umbrella sampling using molecular dynamics simulations. The profile has a deep minimum at the equilibrium position in the bilayer and steeply rises for displacements both deeper into the bilayer and moving away from the bilayer. As the lipid loses contact with the bilayer, the profile abruptly flattens without a significant barrier. The calculated free energy difference of 80 kJ/mol between the minimum of the PMF and the value in water agrees well with the free energy difference calculated from the experimentally measured critical micelle concentration. Significant water/lipid defects form when a lipid is forced into the bilayer interior, in the form of a small water pore that spans the membrane. The energy required to form such a water pore is also found to be 80 kJ/mol. On the basis of this energy, we estimate the lipid flip-flop rate and permeability rate of sodium ions. The resulting rates are in good agreement with experimental measurements, suggesting lipid flip-flop and basal permeability of ions are pore mediated.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Of particular relevance to GARD are molecular dynamics studies that provide detailed information on bilayer entry and exit of individual lipid molecules, including inference on thermodynamic and kinetic parameters [140,255,256].”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [140]
Citations
Cites
LINCS: A linear constraint solver for molecular simulations
Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199709)18:12 · Cited by 18,479
Intermolecular and Surface Forces
Israelachvili, J. N. (2011) · Elsevier eBooks · doi:10.1016/c2009-0-21560-1 · Cited by 8,241
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
Miyamoto, S., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130805 · Cited by 7,268
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130812 · Cited by 6,808
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
Torrie, G. M., & Valleau, J. P. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90121-8 · Cited by 6,091
Interaction Models for Water in Relation to Protein Hydration
Berendsen, H. J. C., Postma, J., A, W. F. V. G., & Hermans, J. (1981) · Jerusalem Symposia on Quantum Chemistry and Biochemistry · doi:10.1007/978-94-015-7658-1_21 · Cited by 5,733
Dynamic strength of molecular adhesion bonds
Evans, E., & Ritchie, K. P. (1997) · Biophysical Journal · doi:10.1016/s0006-3495(97)78802-7 · Cited by 2,556
Berger, O., Edholm, O., & Jähnig, F. (1997) · Biophysical Journal · doi:10.1016/s0006-3495(97)78845-3 · Cited by 1,824
Diversity of antimicrobial peptides and their mechanisms of action
Epand, R. M., & Vogel, H. J. (1999) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/s0005-2736(99)00198-4 · Cited by 1,354
Plasma lipoproteins: apolipoprotein structure and function.
Mahley, R. W., Innerarity, T. L., Rall, S. C., & Weisgraber, K. H. (1984) · Journal of Lipid Research · doi:10.1016/s0022-2275(20)34443-6 · Cited by 1,155
Research works printed but not linked: 14
- Marrink S. J., 2003, J. Am. Chem. Soc., 125, 11145
- Berg O. G., 2001, Chem. Rev., 101, 2653
- Tall A. R., 1986, J. Lipid Res., 27, 367
- Gumperz J. E., 2006, Traffic (Oxford, U.K.), 7, 13
- Kornberg R. D., 1971, Biochem., 10, 20
- Toyoshima Y., 1975, Biochem., 14, 1531
- Essmann U., 1995, J. Chem. Phys., 103, 8593
- Berendsen H. J. C., 1984, J. Chem. Phys., 81, 3690
- Marrink S. J., 2001, J. Am. Chem. Soc., 123, 8639
- Tolpekina T. V., 2004, J. Chem. Phys., 121, 12066
- Leontiadou H., 2005, Modeling Membranes under Stress
- Pohorille A., 2001, Cell. Mol. Biol. Lett., 6, 374
- Deamer D. W., 1997, Bioelectrochem. Bioenerg., 42, 160
- Kol M. A., 2003, J. Biol. Chem., 278, 24593
Cited by
Sorted by citations
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
Marrink, . J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp071097f · Cited by 5,641
Self-citationComputational Modeling of Realistic Cell Membranes
Marrink, . J., Corradi, V., Souza, P. C. T., Ingólfsson, H. I., Tieleman, D. P., & Sansom, M. S. P. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00460 · Cited by 715
Self-citationToroidal pores formed by antimicrobial peptides show significant disorder
Sengupta, D., Leontiadou, H., Mark, A. E., & Marrink, . J. (2008) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2008.06.007 · Cited by 574
Herce, H. D., & Garcı́a, A. E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706574105 · Cited by 488
Abrams, C. F., & Bussi, G. (2013) · Entropy · doi:10.3390/e16010163 · Cited by 441
Metadata
- Authors
- Tieleman, D. P., & Marrink, S.-J.
- Affiliations
- University of Calgary (CA)
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-08-31
- Volume
- 128
- Issue
- 38
- Pages
- 12462-12467
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2121138440
- Cited by
- 230
- References
- 42
- Citations by year
- 2026: 13 · 2025: 9 · 2024: 3 · 2023: 9 · 2022: 1 · 2021: 9 · 2020: 8 · 2019: 16 · 2018: 12 · 2017: 15 · 2016: 16 · 2015: 11 · 2014: 20 · 2013: 9 · 2012: 13
- FWCI
- 6.08
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- other-oa
- Locations
- Journal of the American Chemical Society (publishedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- Alfred P. Sloan Foundation
- Western Canada Research Grid
- Fondation pour la Recherche Médicale
- Canadian Institutes of Health Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- lipid flip-flop, potential of mean force, phospholipid bilayers, water pores, membrane permeability, sodium ion permeation, critical micelle concentration, activation barrier, membrane defects, umbrella sampling
- MeSH terms
- Computer Simulation, Kinetics, Lipid Bilayers, Models, Molecular, Phospholipids, Sodium, Water, 1,2-Dipalmitoylphosphatidylcholine
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
