2009_Book_FoodChemistry

1.4 Proteins 49
small cyclic peptides or in proteins before proline
residues).
Thus in ribonuclease A, two X-Pro bonds
have trans-conformation (Pro-42 and Pro-
117), and two have cis-conformation (Pro-93
and Pro-114). The equilibrium between the
two isomers is catalyzed by specific enzymes
(peptidyl-prolyl-cis/trans-isomerases).
This accelerates the folding of a peptide
chain (cf. 1.4.2.3.2), which in terms of the
biosynthesis occurs initially in all-transconformation.
Six atoms of the peptide bonds, C α i ,C′ i ,O i,N i+1 ,
C α i+1 and H i+1, lie in one plane (cf. Fig. 1.16).
For a trans-peptide bond, ω i is 180 ◦ . The position
of two neighboring planes is determined by the
numerical value of the angles ψ i (rotational bond
between a carbonyl carbon and an α-carbon) and
φ i (rotational bond between an amide-N and an
α-carbon). For an extended peptide chain, ψ i =
180 ◦ and φ i = 180 ◦ . The position of side chains
can also be described by a series of angles χ 1−n
i
.
1.4.2.2 Secondary Structure
(Regular Structural Elements)
The primary structure gives the sequence of
amino acids in a protein chain while the secondary
structure reveals the arrangement of the
chain in space. The peptide chains are not in
an extended or unfolded form (ψ i ,φ i = 180 ◦ ).
It can be shown with models that ψ i and φ i ,
at a permissible minimum distance between
non-bonding atoms (Table 1.20), can assume
only particular angles. Figure 1.17 presents the
Table 1.20. Minimal distances for nonbonded
atoms (Å)
C N O H
C 3.20 a 2.90 2.80 2.40
(3.00) b (2.80) (2.70) (2.20)
N 2.70 2.70 2.40
(2.60) (2.60) (2.20)
O 2.70 2.40
(2.60) (2.20)
H 2.00
(1.90)
a Normal values.
b Extreme values.
Fig. 1.16. Definitions for torsion angles in a peptide
chain
ω i = 0 ◦ for C α i −C′ i /N i+1−C α i+1 → cis,
ψ i = 0 ◦ for C α i −N i/C ′ i −O i → trans,
φ i = 0 ◦ for C ′ i −C′ i /N i−H → trans,
χ i = 0 ◦ for C α i −N iC β i −C i → cis.
The angles are positive when the rotation is clockwise
and viewed from the N-terminal side of a bond
or (for X) from the atom closer to the main chain respectively.
(according to Schulz and Schirmer, 1979)
Fig. 1.17. φ,ψ-Diagram (Ramachandran plot). Allowed
conformations for amino acids with a C β -atom
obtained by using normal (−) and lower limit (- - -)
contact distances for non-bonded atoms, from Table
1.20. β-Sheet structures: antiparallel (1); parallel
(2), twisted (3). Helices: α-, left-handed (4), 3 10 (5),
α, right-handed (6), π (7)