As described in Chapter 2, hydrophobic molecules, including the nonpolar side chains of particular amino acids, tend to be forced together in an aqueous environment in order to minimize their disruptive effect on the hydrogen-bonded network of water molecules (see p. As in the previous figure, R is used as a general (more.)Ī fourth weak force also has a central role in determining the shape of a protein. Although a single one of these bonds is quite weak, many of them often form together to create a strong bonding arrangement, as in the example shown. Three types of noncovalent bonds that help proteins fold. The stability of each folded shape is therefore determined by the combined strength of large numbers of such noncovalent bonds ( Figure 3-5). But many weak bonds can act in parallel to hold two regions of a polypeptide chain tightly together. Individual noncovalent bonds are 30–300 times weaker than the typical covalent bonds that create biological molecules. The weak bonds are of three types: hydrogen bonds, ionic bonds, and van der Waals attractions, as explained in Chapter 2 (see p. These involve atoms in the polypeptide backbone, as well as atoms in the amino acid side chains. The folding of a protein chain is, however, further constrained by many different sets of weak noncovalent bonds that form between one part of the chain and another. By contrast, rotation can occur about (more.) The peptide bond is planar (gray shading) and does not permit rotation.
(A) Each amino acid contributes three bonds (red) to the backbone of the chain.
Conversely, peptidylation with Ac-PhePhe shows a preference for the LL isomer over the DD isomer.Steric limitations on the bond angles in a polypeptide chain. The preference for hydrophobic D-amino acids can be decreased by addition of an organic solvent to the reaction medium. The molecular basis for these preferences for D-isomer is understandable in the light of our previous studies and seems to be due to preferential hydrophobic interaction of the D-isomer with adenine.
Ac-Leu, the gamma-branched amino acid, showed a slightly low D/L ratio relative to its hydrophobicity. The beta-branched amino acids, Ile and Val, showed an extreme preference for D-isomer. All N-acetyl amino acids we studied showed faster reaction of the D-isomer, with a generally decreasing preference for D-isomer as the hydrophobicity of the amino acid decreased. The present studies relate to the D, L preference in the esterification of 5'-AMP. Preferential hydrophobic interactions are responsible for a preference of D-amino acids in the aminoacylation of 5'-AMP with hydrophobic amino acids We have studied the chemistry of aminoacyl AMP to model reactions at the 3' terminus of aminoacyl tRNA for the purpose of understanding the origin of protein synthesis.
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