By Richard W. Pastor, Scott E. Feller (auth.), Kenneth M. Merz Jr., Benoît Roux (eds.)
The interface among a dwelling phone and the encompassing global performs a serious function in different advanced organic approaches. Sperm/egg fusion, virus/cell fusion, exocytosis, endocytosis, and ion permeation are a couple of examples of methods related to membranes. lately, robust instruments equivalent to X-ray crystal lography, electron microscopy, nuclear magnetic resonance, and infra-red and Raman spectroscopy were constructed to represent the constitution and dy namics of biomembranes. regardless of this growth, a few of the elements liable for the functionality of biomembranes are nonetheless no longer good understood. The membrane is a really advanced supramolecular liquid-crystalline constitution that's mostly composed of lipids, forming a bilayer, to which proteins and different biomolecules are anchored. usually, the lipid bilayer atmosphere is pictured as a hydropho bic structureless slab offering a thermodynamic motive force to partition the amino acids of a membrane protein in keeping with their solubility. in spite of the fact that, a lot of the molecular complexity of the phospholipid bilayer atmosphere is missed in one of these simplified view. it truly is most likely that the atomic information of the polar head team quarter and the transition from the majority water to the hydrophobic center of the membrane are very important. An realizing of the criteria liable for the functionality of biomembranes therefore calls for a greater characterization on the molec ular point of ways proteins have interaction with lipid molecules, of the way lipids impact protein constitution and of ways lipid molecules could keep watch over protein function.
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Additional resources for Biological Membranes: A Molecular Perspective from Computation and Experiment
Leiden: ESCOM Science Publishers I. TIME SCALES OF LIPID DYNAMICS AND MOLECULAR DYNAMICS 29 Vaz WLC, Almeida PF (1991): Miscoscopic versus macroscopic diffusion in one-component fluid phase bilayer membranes. Biophys J 60:1553-1554 Venable RM, Zhang Y, Hardy BJ, Pastor RW (1993): Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. Science 262:223-226 Wang CC, Pecora R (1980): Time correlation functions for restricted rotational diffusion. J Chem Phys 72:5333-5340 Wax N (1954): Noise and Stochastic Processes.
An equilibrium angle of 115 was found to reproduce the ab initio result for the minimum structure. This value is similar to the average angle found in crystal structures containing choline (Oelin and Karplus, 1975). The C-C-N-C torsion parameter was adjusted to reproduce the energy difference between the trans minimum energy and the cis transition state structures (see Table 3). 5 kcal/mole above the trans minimum, identical to the MP2/6-3110(d,p)//HF/6-310(d) value. Analysis of changes in the internal geometry (Table 5) in going from the trans to cis orientation showed that the direction of the ab initio trends is reproduced by the CHARMM22 parameters, but that the magnitude of the differences is smaller in the force field calculations.
However, because the differences are unimportant for most of the phospholipid properties of interest, no adjustments were made. Ethanolamine Most of the parameters for the hydroxyl and amine moieties of ethanolamine were extracted from the protein parameters. However, parameters related to the angle and dihedral terms involved in the aliphatic connection between the two moieties do not exist in the protein set. To evaluate these parameters ab initio calculations were performed on the N--C--C-O dihedal surface of ethanolamine; the naming convention used for choline was used for ethanolamine (see Figure 3).