Protein fragments hydration

Short MD runs with a few thousands of water molecules were also carried out to analyze the average hydration of the protein fragments, to detect possible conformational changes due to the solvent and to assess the stability of the geometries found. 

Since DNA is a highly charged polyanion, it is always hydrated by water molecules [in the dry state (under moist air) it contains 12 water molecules per nucleotide subunit]. In a cellular environment, proteins (histones in eukaryotic cells) are always attached to DNA or are at least surrounded by proteins as in viruses. In order to attack DNA, radicals have to be sufficiently mobile in such a partially hydrophilic environment. For this reason, typical lipid radicals confined to the membranes will not be discussed here, although one must keep in mind that small fragments of free-radical nature maybe able to escape the lipid environment and can, in principle, also react with DNA. 

After hydration, a rise in temperature causes disruption of internal structure, for example crystallites in starch or folded structure in proteins. The extent to which this is achieved is determined primarily by a specific cooperative melting event, whose temperature is dependent upon moisture content and applied pressure. If these critical conditions are reached by any part of the flow stream, then shear can cause further fragmentation of both starch granules and the polymers released from them, whereas for proteins or their dissociated subunits, molecular weights remain largely imchanged. A polymer continuous melt is formed in both cases. 

The formation of spanning H-bonded water networks on the surface of biomolecules has been connected with the widely accepted view that a certain amount of hydration water is necessary for the dynamics and function of proteins. Its percolative nature had been suggested first by Careri et al. (59) on the basis of proton conductivity measurements on lysozyme this hypothesis was later supported by extensive computer simulations on the hydration of proteins like lysozyme and SNase, elastine like peptides, and DNA fragments (53). The extremely interesting... 

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