Biomembrane studies, atomic force

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

Li, A., Lee, P. Y, Ho, B., Ding, J. L., and Lim, C. T. 2007. Atomic force microscopy study of the antimicrobial action of sushi peptides on Gram negative bacteria, Biochimica Biophysica Acta-Biomembranes 1768,411-418. 

The atomic force microscope (AFM) is currently used to examine biomembranes and membrane proteins in electrophysiological studies involving the patch-clamp technique (Danker et al. 1997). The structural information of the AFM image may be combined with the functional electrical data (Goksu et al. 2009). Danker et al. (1997) observed three kinds of membrane types, which had different surface morphologies or conducting properties such as the presence of undesired ER. 

More macroscopic phenoipena of biomembranes are trackable by simplification with abandonment of atomic details in the calculations. In a simulation at oil-water interfaces, water and oil molecules are represented by particles labeled w and o , respectively. An amphiphilic molecule such as a lipid is represented by a chain of two w particles followed by five o particles. A completely repulsive interaction is assumed between o and w, and a Lennard-Jones potential is assumed between particles of the same kind. Thus, this simulation is even simpler than the pioneering simulations of atomic chain models described in Section 2.1. Thus, more macroscopic phenomena can be studied easily. Starting from a i patially random distribution of water, oil, and the amphiphilic molecules, the monolayers and micelles composed of the amphiphilic molecules were spontaneously made at oil-water interfaces as shown in Figure 3. Depletion layers between monolayers and micelles were observed, suggesting the repulsion between biomembranes by the solvation force. 

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