Lipids force

Stouch. Based on the Discover force field, Stouch et al. created a lipid force field. It was used in several diffusion studies of DPPC, and of small solutes in a DPPC bilayer, and tested with crystal simulations. A recent test on a crystal using NPT boundary conditions gave good agreement with experimental data. ... 

Fig. VI-6. The force between two crossed cylinders coated with mica and carrying adsorbed bilayers of phosphatidylcholine lipids at 22°C. The solid symbols are for 1.2 mM salt while the open circles are for 10.9 roM salt. The solid curves are the DLVO theoretical calculations. The inset shows the effect of the van der Waals force at small separations the Hamaker constant is estimated from this to be 7 1 x 10 erg. In the absence of salt there is no double-layer force and the adhesive force is -1.0 mN/m. (From Ref. 66.)...

The interest in vesicles as models for cell biomembranes has led to much work on the interactions within and between lipid layers. The primary contributions to vesicle stability and curvature include those familiar to us already, the electrostatic interactions between charged head groups (Chapter V) and the van der Waals interaction between layers (Chapter VI). An additional force due to thermal fluctuations in membranes produces a steric repulsion between membranes known as the Helfrich or undulation interaction. This force has been quantified by Sackmann and co-workers using reflection interference contrast microscopy to monitor vesicles weakly adhering to a solid substrate [78]. Membrane fluctuation forces may influence the interactions between proteins embedded in them [79]. Finally, in balance with these forces, bending elasticity helps determine shape transitions [80], interactions between inclusions [81], aggregation of membrane junctions [82], and unbinding of pinched membranes [83]. Specific interactions between membrane embedded receptors add an additional complication to biomembrane behavior. These have been stud-... 

Finally, Berger et al [192] have developed a teclmique whereby an array of force curves is obtained over the sample surface ( force-curve mapping ), enabling a map of the tip-sample adliesion to be obtained. The autiiors have used this approach to image differently oriented phase domains of Langimiir-Blodgett-deposited lipid films. 

Brandow S L, Turner D C, Ratna B R and Gaber B P 1993 Modification of supported lipid membranes by atomic force microscopy Biophys. J. 64 898... 

Interactions between macromolecules (protems, lipids, DNA,.. . ) or biological structures (e.g. membranes) are considerably more complex than the interactions described m the two preceding paragraphs. The sum of all biological mteractions at the molecular level is the basis of the complex mechanisms of life. In addition to computer simulations, direct force measurements [98], especially the surface forces apparatus, represent an invaluable tool to help understand the molecular interactions in biological systems. 

Protems can be physisorbed or covalently attached to mica. Another method is to innnobilise and orient them by specific binding to receptor-fiinctionalized planar lipid bilayers supported on the mica sheets [15]. These surfaces are then brought into contact in an aqueous electrolyte solution, while the pH and the ionic strength are varied. Corresponding variations in the force-versus-distance curve allow conclusions about protein confomiation and interaction to be drawn [99]. The local electrostatic potential of protein-covered surfaces can hence be detemiined with an accuracy of 5 mV. 

Although extraction of lipids from membranes can be induced in atomic force apparatus (Leckband et al., 1994) and biomembrane force probe (Evans et al., 1991) experiments, spontaneous dissociation of a lipid from a membrane occurs very rarely because it involves an energy barrier of about 20 kcal/mol (Cevc and Marsh, 1987). However, lipids are known to be extracted from membranes by various enzymes. One such enzyme is phospholipase A2 (PLA2), which complexes with membrane surfaces, destabilizes a phospholipid, extracts it from the membrane, and catalyzes the hydrolysis reaction of the srir2-acyl chain of the lipid, producing lysophospholipids and fatty acids (Slotboom et al., 1982 Dennis, 1983 Jain et al., 1995). SMD simulations were employed to investigate the extraction of a lipid molecule from a DLPE monolayer by human synovial PLA2 (see Eig. 6b), and to compare this process to the extraction of a lipid from a lipid monolayer into the aqueous phase (Stepaniants et al., 1997). 

M2irrink et al., 1998] Marrink, S.-J., Berger, O., Tieleman, R, and Jahnig, F. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics dimulations. Biophys. J. 74 (1998) 931-943... 

In this case, only two parameters (k and Iq) per atom pair are needed, and the computation of a quadratic function is less expensive. Therefore, this type of expression is used especially by biomolecular force fields (AMBER, CHARMM, GROMOS) dealing with large molecules like proteins, lipids, or DNA. 

The first molecular dynamics simulations of a lipid bilayer which used an explicit representation of all the molecules was performed by van der Ploeg and Berendsen in 1982 [van dei Ploeg and Berendsen 1982]. Their simulation contained 32 decanoate molecules arranged in two layers of sixteen molecules each. Periodic boundary conditions were employed and a xmited atom force potential was used to model the interactions. The head groups were restrained using a harmonic potential of the form ... 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

Whereas the main challenge for the first bilayer simulations has been to obtain stable bilayers with properties (e.g., densities) which compare well with experiments, more and more complex problems can be tackled nowadays. For example, lipid bilayers were set up and compared in different phases (the fluid, the gel, the ripple phase) [67,68,76,81]. The formation of large pores and the structure of water in these water channels have been studied [80,81], and the forces acting on lipids which are pulled out of a membrane have been measured [82]. The bilayer systems themselves are also becoming more complex. Bilayers made of complicated amphiphiles such as unsaturated lipids have been considered [83,84]. The effect of adding cholesterol has been investigated [85,86]. An increasing number of studies are concerned with the important complex of hpid/protein interactions [87-89] and, in particular, with the structure of ion channels [90-92]. 

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