To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addn. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest nos.
American Institute of Physics. The authors present a new mol. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains const. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liq.
Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties. A Lagrangian formulation is introduced; it can be used to make mol. In this formulation the MD cell shape and size can change according to dynamic equations given by this Lagrangian. This MD technique was used to the study of structural transitions of a Ni single crystal under uniform uniaxial compressive and tensile loads. Some results regarding the stress-strain relation obtained by static calcns.
Under compressive loading, the model of Ni shows a bifurcation in its stress-strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. Such a transition could perhaps be obsd. American Society for Cell Biology.
The transbilayer distribution of many lipids in the plasma membrane and in endocytic compartments is asym. The transbilayer distribution of cholesterol in these membranes is not properly established.
Using the fluorescent sterols, dehydroergosterol and cholestatrienol, and a variety of fluorescence quenchers, we studied the transbilayer distribution of sterols in the plasma membrane PM and the endocytic recycling compartment ERC of a CHO cell line. Sterol fluorescence in the ERC is also quenched efficiently in the permeabilized cells.
In microinjection expts. Bennett, W. Drew; MacCallum, Justin L. The relative stability of cholesterol in cellular membranes and the thermodn.
We used mol. In addn. Our results agree with recent expts. We predicted that the rate of flip-flop is strongly dependent on the compn.
In polyunsatd. We also calcd. In general, cholesterol prefers more ordered and rigid bilayers and has the lowest affinity for bilayers with two polyunsatd. Overall, the simulations provide a detailed mol. An assay was developed to study the spontaneous transfer and transbilayer movement flip-flop of lipid analogs labeled with the fluorescent fatty acid, 5- 5,7-di-Me BODIPY pentanoic acid C5-DMB in large unilamellar lipid vesicles comprised of 1-palmitoyloleoyl phosphatidylcholine POPC.
The assay is based on the concn. A kinetic model was developed to describe the time-dependent changes in concn. These results provide a basis for interpreting the behavior of these lipid analogs in cells.
Nature , , — [ Crossref ], [ PubMed ], [ CAS ], Google Scholar 42 Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension. Lipid bilayer membranes-ubiquitous in biol. Membranes formed from multiple lipid components can laterally sep. This process, which may resemble raft formation in cell membranes, has been directly obsd. Detailed theor. Here we show that high-resoln. Using freely suspended membranes of giant unilamellar vesicles, we are able to optically resolve curvature and line tension interactions of circular, stripe and ring domains.
We observe long-range domain ordering in the form of locally parallel stripes and hexagonal arrays of circular domains, curvature-dependent domain sorting, and membrane fission into sep. By analyzing our observations using available membrane theory, we are able to provide exptl.
Lipids , , 51 — 63 Google Scholar There is no corresponding record for this reference. Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to det.
We investigate the mechanosensitive channel of large conductance MscL from Mycobacterium tuberculosis and aquaporin Z AqpZ and the ammonia channel AmtB from Escherichia coli, using ion mobility mass spectrometry IM-MS , which reports gas-phase collision cross-sections.
We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate PI , in line with its proposed functional role in mechanosensation.
AqpZ is also stabilized by many lipids, with cardiolipin CDL imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar expts. The 2. We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding. Cited By.
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