Hydrophobic effects, protein structure

How then can we account for the high degree of internal order routinely found within globular proteins We believe that combinations of the wide variety of electrostatic interactions reviewed above determine the precise three-dimensional structure of the interior of a protein. We argue that the sum of these interactions produces, at least in part, the enthalpy change on protein folding that is independent of the hydrophobic effect. Crystal structures of small organic compounds provide a useful model of protein interiors, and we now discuss some recent theoretical studies of these systems. 

Protein structure is typically classified as consisting of four levels primary (1°), secondary (11°), tertiary (III°), and quaternary (IV°). Primary structure is the sequence of amino acids in the protein. Secondary structure is the local three-dimensional spatial arrangement of amino acids that are close to one another in the primary sequence. a-Helices and P-sheets compose the majority of secondary structures in all known proteins. Tertiary structure is the spatial arrangement of amino acid residues that are far apart in the linear primary sequence of a single polypeptide chain, and it includes disulfide bonds and noncovalent forces. These noncovalent forces include hydrogen bonding, which is also the primary stabilization force for the formation of a-helices and P-sheets, electrostatic interactions, van der Waals forces, and hydrophobic effects. Quaternary structure is the manner in which subunits of a multi-subunit protein are arranged with respect to one another. 

Protein molecules contain both polar and apolar groups. For proteins dissolved in water, these apolar groups tend to be buried in the interior of the globular structure, as a result of expulsion by the surrounding water. However, other interactions, as well as geometrical constraints, interfere with the hydrophobic effect, so that a minor fraction of the water-accessible surface of the protein molecule may be apolar. Protein molecules that do not spontaneously aggregate in water do not have pronounced apolar patches at their surfaces. 

Szleifer I (1997) Protein adsorption on surfaces with grafted polymers a theoretical approach. Biophys J 72 595-612 Tanford C (1973) The hydrophobic effect. John Wiley Sons, Inc., Hoboken Van Dulm P, Norde W, Lyklema J (1981) Ion participation in protein adsorption at solid surfaces. J Colloid Interf Sci 82 77-82 Zoungrana T, Findenegg GH, Norde W (1997) Structure, stability and activity of adsorbed ensymes. J Colloid Interf Sci 190 437-448 Zoungrana T, Norde W (1997) Thermal stability and enzymatic activity of a-chymotrypsin adsorbed on polystyrene surfaces. Colloid Surf B 9 157-167... 

Hydrophobic interactions are the single most important stabilizing influence of protein native structure. The hydrophobic effect refers to the tendency of non-polar substances to minimize contact with a polar solvent such as water. Non-polar amino acid residues constitute a significant proportion of the primary sequence of virtually all polypeptides. These polypeptides will fold in such a way as to maximize the number of such non-polar residue side chains buried in the polypeptide s interior, i.e. away from the surrounding aqueous environment. This situation is most energetically favourable. 

Physical properties of the protein structure should be considered in designing strategies to achieve stable formulations because they can often yield clues about which solution environment would be appropriate for stabilization. For example, the insulin molecule is known to self-associate via a nonspecific hydrophobic mechanism66 Stabilizers tested include phenol derivatives, nonionic and ionic surfactants, polypropylene glycol, glycerol, and carbohydrates. The choice of using stabilizers that are amphiphilic in nature to minimize interactions where protein hydrophobic surfaces instigate the instability is founded upon the hydro-phobic effect.19 It has already been mentioned that hydrophobic surfaces prefer... 

A series of carboxyl containing bioerodible polymeric materials, characterized by modulated functionality and hydrophobic/hydrophilic balance, was prepared both on a lab-scale and in the pilot plant. Procedures were setup as amenable for scaled-up productions. Those materials displayed a high versatility to combine with proteins in different proportion and to provide hybrid bioerodible matrices without any adverse effect on protein structure and activity. 

Now we can ask what is likely to happen to the three-dimensional structure of a protein if we make a conservative replacement of one amino acid for another in the primary structnre. A conservative replacement involves, for example, substitution of one nonpolar amino acid for another, or replacement of one charged amino acid for another. Intnitively, one would expect that conservative replacements would have rather little effect on three-dimensional protein structure. If an isoleucine is replaced by a valine or leucine, the structnral modification is modest. The side chains of all of these amino acids are hydrophobic and will be content to sit in the molecnlar interior. This expectation is borne out in practice. We have noted earlier that there are many different molecnles of cytochrome c in nature, all of which serve the same basic function and all of which have similar three-dimensional structnres. We have also noted the species specificity of insulins among mammalian species. Here too we find a number of conservative changes in the primary structure of the hormone. Although there are exceptions, as a general rule conservative changes in the primary structnre of proteins are consistent with maintenance of the three-dimensional structures of proteins and the associated biological functions. 

The native conformation of proteins is stabilized by a number of different interactions. Among these, only the disulfide bonds (B) represent covalent bonds. Hydrogen bonds, which can form inside secondary structures, as well as between more distant residues, are involved in all proteins (see p. 6). Many proteins are also stabilized by complex formation with metal ions (see pp. 76, 342, and 378, for example). The hydrophobic effect is particularly important for protein stability. In globular proteins, most hydrophobic amino acid residues are arranged in the interior of the structure in the native conformation, while the polar amino acids are mainly found on the surface (see pp. 28, 76). 

When the urea and thiol are removed by dialysis (see p. 78), secondary and tertiary structures develop again spontaneously. The cysteine residues thus return to a suf ciently close spatial vicinity that disulfide bonds can once again form under the oxidative effect of atmospheric oxygen. The active center also reestablishes itself In comparison with the denatured protein, the native form is astonishingly compact, at 4.5 2.5 nm. In this state, the apolar side chains (yellow) predominate in the interior of the protein, while the polar residues are mainly found on the surface. This distribution is due to the hydrophobic effect (see p. 28), and it makes a vital contribution to the stability of the native conformation (B). 

The van der Waals model of monomeric insulin (1) once again shows the wedge-shaped tertiary structure formed by the two chains together. In the second model (3, bottom), the side chains of polar amino acids are shown in blue, while apolar residues are yellow or pink. This model emphasizes the importance of the hydrophobic effect for protein folding (see p. 74). In insulin as well, most hydrophobic side chains are located on the inside of the molecule, while the hydrophilic residues are located on the surface. Apparently in contradiction to this rule, several apolar side chains (pink) are found on the surface. However, all of these residues are involved in hydrophobic interactions that stabilize the dimeric and hexameric forms of insulin. 

A number of different molecular mechanisms can underpin the loss of biological activity of any protein. These include both covalent and non-covalent modification of the protein molecule, as summarized in Table 3.20. Protein denaturation, for example, entails a partial or complete alteration of the protein s 3-D shape. This is underlined by the disruption of the intramolecular forces that stabilize a protein s native conformation, viz hydrogen bonding, ionic attractions and hydrophobic interactions. Covalent modifications of protein structure that can adversely effect its biological activity are summarized below. 

The folding of proteins into their characteristic three-dimensional shape is governed primarily by noncovalent interactions. Hydrogen bonding governs the formation of a helices and [) sheets and bends, while hydrophobic effects tend to drive the association of nonpolar side chains. Hydrophobicity also helps to stabilize the overall compact native structure of a protein over its extended conformation in the denatured state, because of the release of water from the chain s hydration sheath as the protein... 

Hydrophobic Effects. Hydrogen bonds and van der Waals forces are of major importance in determining the secondary structures formed by fibrous proteins. To understand the complex folded structures found in globular proteins additional types of interactions between amino acid side chains... 

Fig. 5. Protein folding. The unfolded polypeptide chain collapses and assembles to form simple structural motifs such as p-sheets and a-helices by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) structure in this way. Larger proteins and multiple protein assemblies aggregate by recognition and docking of multiple domains (eg, p-barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further structural...

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