Conformation lipids

The strategy in a molecular dynamics simulation is conceptually fairly simple. The first step is to consider a set of molecules. Then it is necessary to choose initial positions of all atoms, such that they do not physically overlap, and that all bonds between the atoms have a reasonable length. Subsequently, it is necessary to specify the initial velocities of all the atoms. The velocities must preferably be consistent with the temperature in the system. Finally, and most importantly, it is necessary to define the force-field parameters. In effect the force field defines the potential energy of each atom. This value is a complicated sum of many contributions that can be computed when the distances of a given atom to all other atoms in the system are known. In the simulation, the spatial evolution as well as the velocity evolution of all molecules is found by solving the classical Newton equations of mechanics. The basic outcome of the simulation comprises the coordinates and velocities of all atoms as a function of the time. Thus, structural information, such as lipid conformations or membrane thickness, is readily available. Thermodynamic information is more expensive to obtain, but in principle this can be extracted from a long simulation trajectory. 

Davis, J. FI. (1983). The description of membrane lipid conformation, order and dynan idsltliyiR. Biochim. 

DPPC/Gramicidin D Mixtures. Experiments to determine the effects of Gramicidin D insertion on lipid conformational order, also illustrate one of the important advantages of the CD2 probe method namely, the ability to discern betveen various sources of disorder (Table V). Spectra of DPPC/Gramicidin mixtures at various... 

The authors reported that the hydrophobic peptide had little influence on the lipid structure, as lipid lateral diffusion rates, lipid conformations, and head group orientations were identical to a neat bilayer. The distance distribution of the phospholipid atoms surrounding the peptide was rather broad, pointing to the absence of special interactions between the peptide and the surrounding phospholipids. 

Seelig J, Seelig A. Lipid conformation in model membranes and biological membranes. Quart. Rev. Biophys. 1980 13 19-61. Brown MF, Thurmond RL, Dodd SW, Otten D, Beyer K. Elastic deformation of membrane bilayers probed by deuterium NMR relaxation. J. Am. Chem. Soc. 2002 124 8471-8484. 

Infrared spectroscopy is largely unaJTected by the aforementioned problems. The technique can be used to study the secondary structure of proteins, both in their native environments, as well as after reconstitution into model membranes. In particular, infrared spectroscopy offers several advantages in studies of protein-lipid interactions. Information about lipid conformation and protein secondary structure can be obtained in a single experiment from the same sample. 

To recognize the major infrared bands due to lipids and understand how these may be used to characterize lipid conformation. 

In this chapter, the application of infrared spectroscopy to a range of biological systems was examined. Appropriate sampling techniques and methods of analysis for these systems were discussed. The important infrared bands associated with lipids were introduced and how these relate to the lipid conformation described. The characteristic infrared bands associated with proteins and peptides were outlined. Infrared spectroscopy may be used to estimate the secondary... 

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