Hydration of Proteins and Polypeptides

Kuntz ID, Kauzmann W (1974) Hydration of proteins and polypeptides. Adv Protein Chem 28 239- 345... 

An alternative description of a molecular solvent in contact with a solute of arbitrary shape is provided by the 3D generalization of the RfSM theory (3D-RISM) which yields the 3D correlation functions of interaction sites of solvent molecules near the solute. It was first proposed in a general form by Chandler, McCoy, and Singer [22] and recently developed by several authors for various systems by Cortis, Rossky, and Friesner [23] for a one-component dipolar molecular liquid, by Beglov and Roux [24, 25] for water and a number of organic molecules in water, and by Hirata and co-workers for water [26, 27], metal-water [26, 28] and metal oxide-water [31] interfaces, orientationally dependent potentials of mean force between molecular ions in a polar molecular solvent [29], ion pairs in aqueous electrolyte [30], and hydration of hydrophobic and hydrophilic solutes alkanes [32], polar molecule of carbon monoxide [33], simple ions [34], protein [35], amino acids and polypeptides [36, 37]. It should be noted that accurate calculation of the solvation thermodynamics for ionic and polar solutes in a polar molecular liquid requires special corrections to the 3D-RISM equations to eliminate the electrostatic artifacts of the supercell treatment employed in the 3D-RISM approach [30, 34]. 

To the best of our knowledge, there is one host which conforms to the structure of an Archimedean dual. Harrison was the first to point out that the quaternary structure of ferritin, a major iron storage protein in animals, bacteria, and plants, corresponds to the structure of a rhombic dodecahedron. [45] This protein, which is approximately 12.5 nm in diameter, consists of 24 identical polypeptide subunits (Fig. 9.18), and holds up to 4500 iron atoms in the form of hydrated ferric oxide with... 

A stabilization model proposed for AMDH by Zaccai et al. (1989) accounts for all of the observations on the stability of this protein and on its solution structure. It is based on the fact that the AMDH solution particles are different in the different solvents in which the enzyme is active, and on the reasonable assumption that the bound water and salt molecules are not associated separately with the polypeptide but as hydrated salt ions. 

Hydration of amino add side-chain and polypeptide main-chain atoms. In Thble 23.4, the hydration of the 15 well-refined proteins given in Thble 19.1 is analyzed in terms of functional groups in main-chains and in side-chains. About 44% of the water molecules are bound to side-chain atoms, 42% to main-chain C=0 and only 14% to main-chain N-H. 

Baer, Hiltner, and colleagues (see Hiltner, 1979, and references cited therein) have used dynamic mechanical analysis to examine the hydration of collagen, elastin, and several polypeptides. A torsional pendulum constructed of the sample was examined for low-frequency (i.e., IHz) mechanical loss as a function of hydration and temperature. A common feature is a dispersion that is absent in the dry protein and appears at... 

This behavior can be seen as complementary to another aspect of protein folding the withdrawal of hydrophobic side chains from solvent. The latter minimizes perturbation by burying those portions of the polypeptide for which water is the poorest solvent. The former minimizes perturbation of solvent by what remains exposed. Not all biological macromolecules show so small an effect. Nucleic acids require for their hydration about twice the amount of water required by globular proteins (for heat capacity measurements comparing protein and tRNA, see Rupley and Siemankowski, 1986). It may be signihcant that DNA, with an extensive hydration shell, undergoes facile hydration-dependent conformational transitions, which are not found for proteins. 

A hybrid approach of the extended scaled particle theory (SPT) and the Poisson-Boltzmann (PB) equation for the solvation free energy of non-polar and polar solutes has been proposed by us. This new method is applied for the hydration free energy of the protein, avian pancreatic polypeptide (36 residues). The contributions form the cavity formation and the attractive interaction between the solute and the solvent to the solvation free energy compensate each other. The electrostatic conffibution is much larger than other terms in this hyelration free energy, because hydrophilic residues are ionized in water. This work is the first step toward further applications of our new method to free energy difference calculation appeared in the stability analysis of protein. 

The physicochemical factors that control dmg penetration include the hydration of the stratum corneum, temperature, pFT, drug concentration, and the molecular characteristics of the penetrant and the vehicle. The stratum corneum is a heterogeneous stmcture containing about 40% protein (keratin, a disul-fide-crosslinked linear polypeptide), about... 

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