Helices and sheets
المؤلف:
Peter Atkins، Julio de Paula
المصدر:
ATKINS PHYSICAL CHEMISTRY
الجزء والصفحة:
ص677-678
2025-12-18
51
Helices and sheets
A right-handed a-helix is illustrated in Fig. 19.28. Each turn of the helix contains 3.6 amino acid residues, so the period of the helix corresponds to 5 turns (18 residues). The pitch of a single turn (the distance between points separated by 360°) is 544 pm. The N-H···O bonds lie parallel to the axis and link every fourth group (so residue i is linked to residues i − 4 and i + 4). All the R groups point away from the major axis of the helix. Figure 19.29 shows the Ramachandran plots for the helical form of polypeptide chains formed from the nonchiral amino acid glycine (R = H) and the chiral amino acid l-alanine (R = CH3). The glycine map is symmetrical, with minima of equal depth at φ =−80°, ψ =+90° and at φ =+80°, ψ =−90°. In contrast, the map for l-alanine is unsymmetrical, and there are three distinct low-energy conformations (marked I, II, III). The minima of regions I and II lie close to the angles typical of right- and left-handed helices, but the former has a lower minimum. This result is consistent with the observation that polypeptides of the naturally occurring L-amino acids tend to form right-handed helices.
Ab-sheet(also called the b-pleated sheet) is formed by hydrogen bonding between two extended polypeptide chains (large absolute values of the torsion angles φ and ψ). Some of the R groups point above and some point below the sheet. Two types of structures can be distinguished from the pattern of hydrogen bonding between the constituent chains.
In an anti-parallel b-sheet (Fig. 19.30a), φ =−139°, ψ = 113°, and the N-H····O atoms of the hydrogen bonds form a straight line. This arrangement is a consequence of the antiparallel arrangement of the chains: every N-H bond on one chain is aligned with a C-O bond from another chain. Antiparallel β-sheets are very common in proteins. In a parallel b-sheet (Fig. 19.30b), φ =−119°, ψ = 113°, and the N-H····O atoms of the hydrogen bonds are not perfectly aligned. This arrangement is a result of the parallel arrangement of the chains: each N-H bond on one chain is aligned with a N-H bond of another chain and, as a result, each C-O bond of one chain is aligned with a C-O bond of another chain. These structures are not common in proteins. Circular dichroism (CD) spectroscopy (Section 14.2) provides a great deal of information about the secondary structure of polypeptides. Consider a helical polypeptide. Not only are the individual monomer units chiral, but so is the helix. Therefore, we expect the α-helix to have a unique CD spectrum. Because β-sheets and random coils also have distinguishable spectral features (Fig. 19.31), circular dichroism is a very important technique for the study of protein conformation.
Fig. 19.28 The polypeptide α helix, with poly-l-glycine as an example. Carbon atoms are shown in green, with nitrogen in blue, oxygen in red, and hydrogen atoms in grey. There are 3.6 residues per turn, and a translation along the helix of 150 pm per residue, giving a pitch of 540 pm. The diameter (ignoring side chains) is about 600 pm.
Fig. 19.29 Contour plots of potential energy against the torsional angles ψ and φ, also known as Ramachandran plots, for (a) a glycyl residue of a polypeptide chain and (b) an alanyl residue. The darker the shading is, the lower the potential energy. The glycyl diagram is symmetrical, but regions I and II in the correspond to right- and left-handed helices, are unsymmetrical, and the minimum in region I lies lower than that in region II. (After D.A. Brant and P.J. Flory, J. Mol. Biol. 23, 47 (1967).)
Fig. 19.30 The two types of β-sheets: (a) antiparallel (φ =−139°, ψ = 113°), in which the N-H-O atoms of the hydrogen bonds form a straight-line; (b) parallel (φ =−119°, ψ=113°in which the N-H····O atoms of the hydrogen bonds are not perfectly aligned.
Fig. 19.31 Representative CD spectra of polypeptides. Random coils, α-helices, and β-sheets have different CD features in the spectral region where the peptide link absorbs.
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