SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol

2018 ◽  
Vol 15 (1) ◽  
pp. 762-774 ◽  
Author(s):  
Sangjae Seo ◽  
Wataru Shinoda
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Domain Formation

scholarly journals Domain Formation Induced by the Adsorption of Charged Proteins on Mixed Lipid Membranes

2005 ◽  
Vol 88 (3) ◽  
pp. 1702-1714 ◽  
Author(s):  
Emmanuel C. Mbamala ◽  
Avinoam Ben-Shaul ◽  
Sylvio May
Keyword(s):  
Lipid Membranes ◽  
Domain Formation ◽  
Mixed Lipid Membranes

scholarly journals Modeling nanoparticle wrapping or translocation in bilayer membranes

Nanoscale ◽  
2015 ◽  
Vol 7 (34) ◽  
pp. 14505-14514 ◽  
Author(s):  
Emily M. Curtis ◽  
Amir H. Bahrami ◽  
Thomas R. Weikl ◽  
Carol K. Hall
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Lipid Membranes ◽  
Molecular Level ◽  
Bilayer Membranes

The molecular level interaction between nanoparticles and lipid membranes, including wrapping, is simulated using discontinuous molecular dynamics with the LIME force field.

scholarly journals The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e28637 ◽  
Author(s):  
Mario Orsi ◽  
Jonathan W. Essex
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Coarse Grain

scholarly journals Phospholipid Chain Interactions with Cholesterol Drive Domain Formation in Lipid Membranes

2018 ◽  
Vol 114 (11) ◽  
pp. 2595-2605 ◽  
Author(s):  
W. F. Drew Bennett ◽  
Joan-Emma Shea ◽  
D. Peter Tieleman
Keyword(s):  
Lipid Membranes ◽  
Domain Formation

Interaction of linear polyamines with negatively charged phospholipids: the effect of polyamine charge distance

2014 ◽  
Vol 395 (7-8) ◽  
pp. 769-778 ◽  
Author(s):  
Sebastian Finger ◽  
Christian Schwieger ◽  
Ahmad Arouri ◽  
Andreas Kerth ◽  
Alfred Blume
Keyword(s):  
Phase Transition ◽  
Lipid Membranes ◽  
Electrostatic Interactions ◽  
Lipid Vesicles ◽  
Molecular Crowding ◽  
Domain Formation ◽  
Phase Transition Behavior ◽  
Scanning Calorimetry ◽  
Methylene Groups ◽  
Gel Phase

Abstract The binding of cationic polyamines to negatively charged lipid membranes is driven by electrostatic interactions and additional hydrophobic contributions. We investigated the effect of polyamines with different number of charges and charge separation on the phase transition behavior of vesicles of phosphatidylglycerols (dipalmitoylphosphatidylglycerol and dimyristoylphosphatidylglycerol) to differentiate between effects caused by the number of charges, the charge distance, and the hydrophobicity of the methylene spacer. Using differential scanning calorimetry and Fourier transform infrared spectroscopy complemented with monolayer experiments, we found that the binding constant of polyamines to negatively charged lipid vesicles depends as expected on the number of charges. However, for diamines, the effect of binding on the main phase transition of phosphatidylglycerols (PGs) is also strongly influenced by the charge distance between the ammonium groups in the backbone. Oligoamines with charges separated by two or three methylene groups bind more strongly and have larger stabilizing effects on the lipid gel phase of PGs. With multivalent polyamines, the appearance of several transition peaks points to effects of molecular crowding on the surface, i.e., binding of only two or three charges to the surface in the case of spermine, and possible concomitant domain formation.

Modeling DMPC lipid membranes with SIRAH force-field

2017 ◽  
Vol 23 (9) ◽  
Author(s):  
Exequiel E. Barrera ◽  
Ezequiel N. Frigini ◽  
Rodolfo D. Porasso ◽  
Sergio Pantano
Keyword(s):  
Force Field ◽  
Lipid Membranes

scholarly journals The SPICA Coarse-Grained Force Field for Proteins and Peptides

2021 ◽  
Author(s):  
Shuhei Kawamoto ◽  
Huihui Liu ◽  
Sangjae Seo ◽  
Yusuke Miyazaki ◽  
Mayank Dixit ◽  
...  
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Free Energies ◽  
Transmembrane Peptides ◽  
Energy Profiles ◽  
Protein Model ◽  
Preliminary Version

ABSTRACTA coarse-grained (CG) model for peptides and proteins was developed as an extension of the SPICA (Surface Property fItting Coarse grAined) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulation with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. The side chain analogs reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable dimerization free energies in water compared to those from AA-MD. A series of peptides/proteins adsorbed or penetrated into the membrane simulated by the CG-MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins comparable to those in the orientation of protein in membrane (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated a good performance of the SPICA FF.

scholarly journals Certain, but Not All, Tetraether Lipids from the Thermoacidophilic Archaeon Sulfolobus acidocaldarius Can Form Black Lipid Membranes with Remarkable Stability and Exhibiting Mthk Channel Activity with Unusually High Ca2+ Sensitivity

2021 ◽  
Vol 22 (23) ◽  
pp. 12941
Author(s):  
Alexander Bonanno ◽  
Parkson Lee-Gau Chong
Keyword(s):  
Plasma Membrane ◽  
Potassium Channels ◽  
Lipid Membranes ◽  
Critical Role ◽  
Sulfolobus Acidocaldarius ◽  
Domain Formation ◽  
Channel Activity ◽  
Black Lipid Membranes ◽  
Lipid Species ◽  
Tetraether Lipids

Bipolar tetraether lipids (BTL) have been long thought to play a critical role in allowing thermoacidophiles to thrive under extreme conditions. In the present study, we demonstrated that not all BTLs from the thermoacidophilic archaeon Sulfolobus acidocaldarius exhibit the same membrane behaviors. We found that free-standing planar membranes (i.e., black lipid membranes, BLM) made of the polar lipid fraction E (PLFE) isolated from S. acidocaldarius formed over a pinhole on a cellulose acetate partition in a dual-chamber Teflon device exhibited remarkable stability showing a virtually constant capacitance (~28 pF) for at least 11 days. PLFE contains exclusively tetraethers. The dominating hydrophobic core of PLFE lipids is glycerol dialky calditol tetraether (GDNT, ~90%), whereas glycerol dialkyl glycerol tetraether (GDGT) is a minor component (~10%). In sharp contrast, BLM made of BTL extracted from microvesicles (Sa-MVs) released from the same cells exhibited a capacitance between 36 and 39 pF lasting for only 8 h before membrane dielectric breakdown. Lipids in Sa-MVs are also exclusively tetraethers; however, the dominating lipid species in Sa-MVs is GDGT (>99%), not GDNT. The remarkable stability of BLMPLFE can be attributed to strong PLFE–PLFE and PLFE–substrate interactions. In addition, we compare voltage-dependent channel activity of calcium-gated potassium channels (MthK) in BLMPLFE to values recorded in BLMSa-MV. MthK is an ion channel isolated from a methanogenic that has been extensively characterized in diester lipid membranes and has been used as a model for calcium-gated potassium channels. We found that MthK can insert into BLMPLFE and exhibit channel activity, but not in BLMSa-MV. Additionally, the opening/closing of the MthK in BLMPLFE is detectable at calcium concentrations as low as 0.1 mM; conversely, in diester lipid membranes at such a low calcium concentration, no MthK channel activity is detectable. The differential effect of membrane stability and MthK channel activity between BLMPLFE and BLMSa-MV may be attributed to their lipid structural differences and thus their abilities to interact with the substrate and membrane protein. Since Sa-MVs that bud off from the plasma membrane are exclusively tetraether lipids but do not contain the main tetraether lipid component GDNT of the plasma membrane, domain segregation must occur in S. acidocaldarius. The implication of this study is that lipid domain formation is existent and functionally essential in all kinds of cells, but domain formation may be even more prevalent and pronounced in hyperthermophiles, as strong domain formation with distinct membrane behaviors is necessary to counteract randomization due to high growth temperatures while BTL in general make archaea cell membranes stable in high temperature and low pH environments whereas different BTL domains play different functional roles.

scholarly journals Effect of Line Tension on the Lateral Organization of Lipid Membranes

2007 ◽  
Vol 282 (46) ◽  
pp. 33537-33544 ◽  
Author(s):  
Ana J. García-Sáez ◽  
Salvatore Chiantia ◽  
Petra Schwille
Keyword(s):  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Acyl Chain ◽  
Line Tension ◽  
Theoretical Work ◽  
Time Lapse ◽  
Domain Growth ◽  
Domain Formation ◽  
Membrane Organization ◽  
Cellular Membranes

The principles of organization and functioning of cellular membranes are currently not well understood. The raft hypothesis suggests the existence of domains or rafts in cell membranes, which behave as protein and lipid platforms. They have a functional role in important cellular processes, like protein sorting or cell signaling, among others. Theoretical work suggests that the interfacial energy at the domain edge, also known as line tension, is a key parameter determining the distribution of domain sizes, but there is little evidence of how line tension affects membrane organization. We have investigated the effects of the line tension on the formation and stability of liquid ordered domains in model lipid bilayers with raft-like composition by means of time-lapse confocal microscopy coupled to atomic force microscopy. We varied the hydrophobic mismatch between the two phases, and consequently the line tension, by modifying the thickness of the disordered phase with phosphatidylcholines of different acyl chain length. The temperature of domain formation, the dynamics of domain growth, and the distribution of domain sizes depend strongly on the thickness difference between the domains and the surrounding membrane, which is related to line tension. When considering line tension calculated from a theoretical model, our results revealed a linear increase of the temperature of domain formation and domain growth rate with line tension. Domain budding was also shown to depend on height mismatch. Our experiments contribute significantly to our knowledge of the physical-chemical parameters that control membrane organization. Importantly, the general trends observed can be extended to cellular membranes.

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