Download Advances in Computational Biology by Hugo O. Villar (Eds.) PDF

By Hugo O. Villar (Eds.)

The second one quantity in a sequence which goals to target advances in computational biology. This quantity discusses such issues as: statistical research of protein sequences; growth in large-scale series research; and the structure of loops in proteins

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The dissociation constant k^^ can, in this case, be estimated from (Huang, 1986) where g* is the free energy of activation, which is the energy required to break the hydrogen bonds linking two monomers, and v is a frequency factor almost independent of temperature. Here we analyze dimer formation on a phenomenological microscopic level. A. suitably modified to account for the coupling to lipid molecules of the gramicidin monomers or dimers incorporated in the bilayers. By analogy with the interactions between the acyl chains, the interactions between lipid molecules of species A and gramicidin monomers G are then written as 2 i^^G=X a^l r.

As a consequence, the composition profile away from the protein surface displays a pronounced oscillatory behavior dictated by the diffusional processes and the mass conservation law. After introduction of the proteins to the initially equilibrated mixture, the protein surfaces are, on a time scale corresponding to short-range diffusion, enriched in the appropriate species whose hydrophobic acyl-chain length is compatible with the protein thickness. However, on this time scale, the mixture does not have time to reorganize fully and to compensate for the excess mass of the enriched species.

This is reasonable because ionic channels are usually observed in the fluid phase of lipid bilayers and the channel-forming monomers are usually much larger than lipid molecules. III. COMPUTER-SIMULATION TECHNIQUES A. Monte Carlo Computer-Simulation Techniques A full description of the implementation of standard Monte Carlo simulations will not be given, but we refer the reader to general references on this subject (Mouritsen, 1984 and 1990). We shall, however, concentrate on describing several new techniques which are extremely powerful for characterizing phase equilibria in lipid bilayers and lipid-protein systems when combined with Monte Carlo simulations.

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