Noncovalent hydrophobic effects

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces 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) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -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 stmctural...

Nonpolar molecules tend to have low solubilities in water, and large nonpolar solutes tend to form aggregates in aqueous solution. In the past these tendencies were sometimes explained by invoking a special hydrophobic bond between nonpolar groups. However, bond is a misnomer here, and it is better to refer to an effect, because there is no exchange of bonding electrons involved in either of the tendencies noted above. Instead, the hydrophobic effect is a combination of several of the fundamental noncovalent interactions, and it involves details of the organization of water molecules around nonpolar solute molecules. 

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... 

While technically simpler than the covalent approach, the self-assembly approach creates more heterogeneous sites and also requires templates with specific functional groups.8 Since sol-gel chemistry is aqueous based, H-bonding interactions are significantly weaker compared to the conventional organic polymerization methods. Often, hydrophobic effects and ionic interactions are utilized. A number of other examples of the noncovalent approach to imprinting in sol-gel-derived materials are provided in recent reviews.5 17 In the sections below, the focus will be on some of the newer aspects of small molecule imprinting in silica that involve the use of chiral templates... 

We review the subject of noncovalent interactions in proteins with particular emphasis on the so-called weakly polar interactions. First, the physical bases of the noncovalent electrostatic interactions that stabilize protein structure are discussed. Second, the four types of weakly polar interactions that have been shown to occur in proteins are described with reference to some biologically significant examples of protein structure stabilization and protein-ligand binding. Third, hydrophobic effects in proteins are discussed. Fourth, an hypothesis regarding the biological importance of the weakly polar interaction is advanced. Finally, we propose adoption of a systematic classification of electrostatic interactions in proteins. 

Hydrophobic effect. The noncovalent association of nonpolar groups with each other in aqueous solution. 

Protein tertiary (111°) structure The overall three-dimensional structure of a single polypeptide chain, including positions of disulfide bonds. Noncovalent forces such as hydrogen bonding, electrostatic forces, and hydrophobic effects are also important. 

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. 

Biochemists distinguish four levels of the structural organization of proteins. In primary structure, the amino acid residues are connected by peptide bonds. The secondary structure of polypeptides is stabilized by hydrogen bonds. Prominent examples of secondary structure are a-helices and / -pleated sheets. Tertiary structure is the unique three-dimensional conformation that a protein assumes because of the interactions between amino acid side chains. Several types of interactions stabilize tertiary structure the hydrophobic effect, electrostatic interactions, hydrogen bonds, and certain covalent bonds. Proteins that consists of several separate polypeptide subunits exhibit quaternary structure. Both noncovalent and covalent bonds hold the subunits together. 

Four main types of noncovalent Interactions occur In biological systems Ionic bonds, hydrogen bonds, van der Waals Interactions, and Interactions due to the hydrophobic effect. 

None of these five categories of noncovalent forces can be completely separated out from all of the others. Van der Waals interactions continue to play a part in each of the other four phenomena. Hydrogen bonds can be considered as a special case of ionic interactions, and the hydrophobic effect tends to reflect hydrogen bonding in the solvent. Therefore, it is informative to discuss each of these categories separately so as to focus on their unique properties. 

Spolar, R., et al. (1989). Hydrophobic Effect in Protein Folding and Other Noncovalent Processes Involving Proteins, PNAS 86 8382-8385. 

Lipids are amphipathic inolecules composed of a polar, hydrophilic head connected to a nonpolar, hydrophobic hydrocarbon tail. When in an aqueous environment, lipids tend to associate noncovalently. There are two driving forces for this association the hydrophobic effect due to the nonpolar tails, and the van der Waals interactions between the hydrocarbon portions of the molecules. This behavior in water can cause lipids to spontaneously form surface monolayers, bilayers, micelles, or vesicles, depending on the structures of the head and tail of the lipid molecule. We shall direct our attention here to the cell membrane bilayer, the most important of these biological assemblies. 

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