Side-chain interactions hydrogen bond

A putative packing arrangement in the monoclinic unit cell (Fig. 40b) reveals that there are no direct interactions among the main chains of adjacent helices. However, the peripheral side chains form hydrogen bonds with both main and side chains. As in the case of 46, the ordered structure of 47 supports the hypothesis that side chains often promote the formation of stable, branched polysaccharide helices. 

EXAMPLE 2.4 Proteins are polymers of polar and nonpolar amino acids the amino acid nnits in the polymer are called residues becanse when the peptide bond between an amino acid and a peptide is formed, water is removed in a condensation reaction, leaving a residne of the amino acid. Amino acid residnes that have polar side chains form hydrogen bonds with water so they are hydrophilic (Fig. 2-5). Nonpolar side chains of amino acid residnes do not form hydrogen bonds with water, so they do not dissolve readily in it they are said to be hydrophobic. Thns proteins tend to fold np so that their hydrophobic residnes are clnstered in an interior core, away from contact with the aqneons environment and the hydrophilic residnes tend to be arranged on the exterior interacting with water. Interactions also occnr with other proteins and other biomolecnles in general. 

Figure 21.31 shows the proposed interaction between exemestane and the aromatase eazyme. The stmcture of exemestane is close to that of androstenedione and it fits the active site of the enzyme very closely, interacting with the lipophilic phenylalanine and isoleucine side chains and hydrogen bonding to serine 478. However, because... 

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

Another ionic liquid, containing a nonyl-rather than a butyl-side chain, is shown in Figure 4.2-2. There is little difference between the basic structures of these two ion-pairs (Figures 4.2-1 and 4.2-2) with respect to the non-bonded interactions (hydrogen bonds) occurring between the F atoms on the anion and the C-H moieties on the imidazolium cation. 

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