Proteins polar interactions

In addition to the restrictions on their mobiHty caused by steric and polar interactions between chemical groups, the protein molecules in wool fibers are covalentiy cross-linked by disulfide bonds. Permanent setting only occurs if these disulfide bonds are also rearranged to be in equiHbrium with the new shape of the fiber. Disulfide bond rearrangement occurs only at high temperature (>70° C) in wet wool and at even higher temperatures (above 100°C) in... 

If the protein of interest is a heteromultimer (composed of more than one type of polypeptide chain), then the protein must be dissociated and its component polypeptide subunits must be separated from one another and sequenced individually. Subunit associations in multimeric proteins are typically maintained solely by noncovalent forces, and therefore most multimeric proteins can usually be dissociated by exposure to pEI extremes, 8 M urea, 6 M guanidinium hydrochloride, or high salt concentrations. (All of these treatments disrupt polar interactions such as hydrogen bonds both within the protein molecule and between the protein and the aqueous solvent.) Once dissociated, the individual polypeptides can be isolated from one another on the basis of differences in size and/or charge. Occasionally, heteromultimers are linked together by interchain S—S bridges. In such instances, these cross-links must be cleaved prior to dissociation and isolation of the individual chains. The methods described under step 2 are applicable for this purpose. 

The subunits of an oligomeric protein typically fold into apparently independent globular conformations and then interact with other subunits. The particular surfaces at which protein subunits interact are similar in nature to the interiors of the individual subunits. These interfaces are closely packed and involve both polar and hydrophobic interactions. Interacting surfaces must therefore possess complementary arrangements of polar and hydrophobic groups. 

Burley SK, Petsko GA. Weakly polar interactions in proteins. Protein Chem 1988 39 125-192. 

The 15N spectral peaks of fully hydrated [15N]Gly-bR, obtained via cross-polarization, are suppressed at 293 K due to interference with the proton decoupling frequency, and also because of short values of T2 in the loops.208 The motion of the TM a-helices in bR is strongly affected by the freezing of excess water at low temperatures. It is shown that motions in the 10-j-is correlation regime may be functionally important for the photocycle of bR, and protein-lipid interactions are motionally coupled in this dynamic regime. 

Within the promoter there can be subtle structural differences that influence the polar interaction with the protein. For example, Figure 5 illustrates the cyclic voltammograms of cytochrome c obtained at a gold electrode modified with isomers of pyridine-carboxylaldehyde-thiosemi-carbazone (PATS). 

Polarization interactions for atoms and small molecules or functional groups are much weaker than the other interactions listed above. For example, in vacuum the attractive energy between two methyl groups is only about 0.15 kcal/mol (0.6 kJ/mol) at a separation of 0.4 nm. However, polarization interactions are additive, so that for large bodies with many individual polarization interactions (e.g., a protein binding a large substrate molecule) the overall contribution may be 10 to 20 kcal/mol (40-80 kJ/mol). Furthermore, these interactions will be present for both nonpolar and polar (even ionic) groups. 

Where this factor plays a role, the hydrophobic interaction between the hydrocarbon chains of the surfactant and the non-polar parts of protein functional groups are predominant. An example of this effect is the marked endothermic character of the interactions between the anionic CITREM and sodium caseinate at pH = 7.2 (Semenova et al., 2006), and also between sodium dodecyl sulfate (SDS) and soy protein at pH values of 7.0 and 8.2 (Nakai et al., 1980). It is important here to note that, when the character of the protein-surfactant interactions is endothermic (/.< ., involving a positive contribution from the enthalpy to the change in the overall free energy of the system), the main thermodynamic driving force is considered to be an increase in the entropy of the system due to release into bulk solution of a great number of water molecules. This entropy... 

Figure 6.8 Sketch of proposed molecular mechanism of protein-surfactant interaction for CITREM + sodium caseinate (0.5 % w/v in aqueous medium (pH = 7.2, ionic strength = 0.05 M) at 293 K. Picture (I) shows the water molecules bound with polar groups of the protein and surfactant, as w ell as w ater molecules structured as a result of hydrophobic hydration around the hydrocarbon chain of the surfactant. (For clarity, the free w ater molecules are not shown.) Picture (H) demonstrates the release of bound and structured water molecules resulting Rom the predominantly hydrophobic interactions between protein and surfactant. Reproduced Rom Semenova et al. (2006) with permission.

Water binding varies with the number and type of polar groups (5 ). Other factors that affect the mechanism of protein-water interactions include protein conformation and environmental factors that affect protein polarity and/or conformation. Conformational changes in the protein molecules can affect the nature and availability of the hydration sites. Transition from globular to random coil conformation may expose previously buried amino acid side chains, thereby making them available to interact with aqueous medium. Consequently, an unfolded conformation may permit the protein to bind more water than was possible in the globular form ( ). 

Amino acids with nonpolar (hydrophobic) R-groups are generally found in the interior of proteins that function in an aqueous environment, and on the surface of proteins (such as membrane proteins) that interact with lipids. Amino acids with polar side chains are gener ally found on the outside of proteins that function in an aqueous environment, and in the interior of membrane-associated proteins. 

However, it was immediately recognized by peptide chemists that, even in the cases where a direct (backbone)peptide -protein(backbone) interaction is not operative, the backbone conformation may dramatically influence the biological response. It is evident that the introduction of new, promising peptidomimetics is based primarily on the combined knowledge of the complementary conformational, topochemical, and electronic properties of the native peptide and of its address (in other words, of the receptor or the active site of the enzyme with which it interacts). Then, the design of peptidomimetics as potential bioactive compounds must take into particular account two structural factors (i) a favorable fit (tertiary structure) with respect to the corresponding complementary spatial situation at the active site (ii) the placement of structural elements (e.g., functional groups, polar and... 

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