Protein hydration, mechanisms

Figure 46. A unified molecular mechanism of protein hydration dynamics and coupled water-protein fluctuations. The initial ultrafast dynamics in a few picoseconds (ii) represents local collective orientation or small translation motions, which mainly depend on local electrostatic interactions. On the longer time (12), the water networks undergo structural rearrangements in the layer, which are strongly coupled with both protein fluctuations and bulk-water dynamic exchange.

Because of the ease with which molecular mechanics calculations may be obtained, there was early recognition that inclusion of solvation effects, particularly for biological molecules associated with water, was essential to describe experimentally observed structures and phenomena [32]. The solvent, usually an aqueous phase, has a fundamental influence on the structure, thermodynamics, and dynamics of proteins at both a global and local level [3/]. Inclusion of solvent effects in a simulation of bovine pancreatic trypsin inhibitor produced a time-averaged structure much more like that observed in high-resolution X-ray studies with smaller atomic amplitudes of vibration and a fewer number of incorrect hydrogen bonds [33], High-resolution proton NMR studies of protein hydration in aqueous... 

The purpose of the present analysis is two-fold (i) to examine the local composition of a mixed solvent around different proteins in dilute solutions of proteins in water/PEG mixed solvents as a function of the PEG concentration and molecular weight and to use the obtained results to identify the mechanism of protein hydration in the presence of PEG, and (u) to predict the solubility of proteins in water/PEG mixed solvents. Finally, the obtained results are compared with experiments available in the literature. 

In this chapter we discuss the structure of this H-bond network, examining recent experiments on hydration mechanisms of macromolecules that have contributed original information on the structures of H-bond networks developed by H2O molecules in these macromolecules. We then describe present experiments on bioprotection that stress the impact this H-bond network has on the structure of the macromolecule itself, before mentioning protein folding, which have undergone rapid development in recent years, but have not yet reached a point where significant information could be obtained. We then proceed... 

The H-bond networks of hquid water and ice are very dense and extend over a very large region. All water molecules are part of these networks and nearly all of them are tetra-coordinated. This is not so in macromolecules where many different situations can be encountered, following the density of hydrophilic groups this macromolecule exhibits and also the state of hydration of the macromolecule, that is the number of H2O molecules that are embedded in it. Some recent experiments conveyed information on the structures of the H-bond networks in these systems. They are experiments on hydration mechanisms, lyo or cryoprotection, and folding of proteins. These relatively few mechanisms that have been recently studied in some detail are described in this section. They give what could be called a preview on this H-bond network developed by H2O molecules in macromolecules. 

In addition to the two examples described above, IR spectrometric methods have been applied to a few proteins, such as bovine serum albumin (BS A) (14,15) or lysozyme (16). They provided hydration mechanisms similar to those described above, but the relation between the determined structure of the H-bond network at a definite hygrometry and properties of... 

Whatever the coupling agent is, the control of non-specific protein absorption is important to the use of nanomaterials in specific protein binding. There are plenty of molecules used for protection of various surfaces from proteins with mechanisms as steric repulsion, hydration and solvent structuring. For example, the modification of CNTs with the absorption of biotinylated Tween 20 allowed streptavidin recognition by the specific biotin-streptavidin interaction, but provided resistance towards other protein absorption [133]. 

As we shall see, present knowledge of water structure can help explain many aspects of a number of biological events—for example, membrane transport, charge transfer, protein hydration, and the mechanism of action of anesthetics. 

Low, P.S., Somero, G.N. Protein hydration changes during catalysis a new mechanism of enzyme rate-enhancement and ion activation/inhibition of catalysis. Proc. Natl. Acad. Sci. U.S.A. 1975, 72(9), 3305-3309. 

The simplicity and accuracy of such models for the hydration of small molecule solutes has been surprising, as well as extensively scrutinized (Pratt, 2002). In the context of biophysical applications, these models can be viewed as providing a basis for considering specific physical mechanisms that contribute to hydrophobicity in more complex systems. For example, a natural explanation of entropy convergence in the temperature dependence of hydrophobic hydration and the heat denaturation of proteins emerges from this model (Garde et al., 1996), as well as a mechanistic description of the pressure dependence of hydrophobic... 

Figure 3. Mechanism of microsomal EH-catalyzed hydration of the K-region epoxide enantiomers of BA, BaP, and DMBA. The percentages of the trans-addition product by water for each enantiomeric epoxide are indicated. The enantiomeric composition of the dihydrodiol enantiomers formed from the hydration of DMBA 5S,6R-epoxide was determined using 1 mg protein equivalent of liver microsomes from pheno-barbital-treated rats per ml of incubation mixture and this hydration reaction is highly dependent on the concentration of the microsomal EH (49). The epoxide enantiomer formed predominantly from the respective parent hydrocarbon by liver microsomes from 3-methylcho-lanthrene-treated rats is shown in the box.

In summary, the physiological control of silk protein conversion shows an ingenious balance of activating and inhibiting mechanisms that are dependent on composition and sequence arrangement (Krejchi et al., 1994). Denaturing effects observed in silks appear to be identical to those found in amyloid-forming proteins, and they principally alter the competitive outcome of the hydration of nonpolar and polar residues (Anfinsen, 1973 Dill, 1990 Dobson and Karplus, 1999 Kauzmann, 1959). The key differences to amyloids may lie in the hierarchical level of the structures (Muthukumar et al., 1997) involved in the assembly of silks compared to amyloids. 

Cleavage of the oxirane C-0 bond produces a zwitterionic intermediate (Fig. 10.22), which that can undergo chloride shift (Pathway a) to 2,2-dich-loroacetyl chloride (10.90) followed by hydrolysis to 2,2-dichloroacetic acid (10.91). Furthermore, the zwitterionic intermediate reacts with H20 or H30+ (Pathway b) by pH-independent or a H30+-dependent hydrolysis, respectively. The pH-independent pathway only is shown in Fig. 10.22, Pathway b, but the mechanism of the H30+-dependent hydrolysis is comparable. Hydration and loss of Cl, thus, leads to glyoxylyl chloride (10.92), a reactive acyl chloride that is detoxified by H20 to glyoxylic acid (10.93), breaks down to formic acid and carbon monoxide, or reacts with lysine residues to form adducts with proteins and cytochrome P450 [157], There is also evidence for reaction with phosphatidylethanolamine in the membrane. 

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