Page 75 - Color Atlas of Biochemistry
P. 75
66 Biomolecules
Peptide bonds example, the peptide hormone angiotensin II
(see p. 330) has the sequence Asp-Arg-Val-
Tyr-Ile-His-Pro-Phe, or DRVYIHPF.
A. Peptide bond
The amino acid components of peptides and
proteins are linked together by amide bonds D. Conformational space of the peptide
(see p. 60) between α-carboxyl and α-amino chain
groups. This type of bonding is therefore also With the exception of the terminal residues,
known as peptide bonding.In the dipeptide every amino acid in a peptide is involved in
shown here, the serine residue has a free two peptide bonds (one with the preceding
ammonium group, while the carboxylate residueand onewith the following one).Due
group in alanine is free. Since the amino acid to the restricted rotation around the C–N
+
with the free NH 3 group is named first, the bond, rotations are only possible around the
peptide is known as seryl alanine,orin abbre- N–C α and C α –C bonds (2). As mentioned
viated form Ser-Ala or SA. above, these rotations are described by the
dihedral angles φ (phi) and ψ (psi). The angle
describes rotation around the N–C α bond; ψ
B. Resonance
describes rotation around C α –C—i. e., the po-
Like all acid–amide bonds, the peptide bond is sition of the subsequent bond.
stabilized by resonance (see p. 4). In the con- For steric reasons, only specific combina-
ventional notation (top right) it is represented tions of the dihedral angles are possible.
as a combination of a C=O double bond with a These relationships can be illustrated clearly
C–N single bond. However, a C=N double bond by a so-called φ/ψ diagram (1). Most combi-
with charges at O and N could also be written nations of φ and ψ are sterically “forbidden”
(middle). Both of these are only extreme cases (red areas). For example, the combination φ =
of electron distribution, known as resonance 0° and ψ =180° (4)would placethe two
structures. In reality, the π electrons are carbonyl oxygen atoms less than 115 pm
delocalized throughout all the atoms (bot- apart—i. e., at a distance much smaller than
tom). As a mesomeric system, the peptide the sum of their van der Waals radii (see p. 6).
bond is planar.Rotation aroundthe C–N Similarly, in the case of φ =180°and ψ =0° (5),
bond would only be possible at the expense the two NH hydrogen atoms would collide.
of large amounts of energy, and the bond is The combinations located within the green
therefore not freely rotatable. Rotations are areasare the onlyonesthat are sterically
only possible around the single bonds marked feasible (e. g., 2 and 3). The important secon-
with arrows. The state of these is expressed dary structures that are discussed in the fol-
using the angles φ and ψ (see D). The plane in lowing pages are also located in these areas.
which the atoms of the peptide bond lie is The conformations located in the yellow areas
highlighted in light blue here and on the fol- are energetically less favorable, but still pos-
lowing pages. sible.
The φ/ψ diagram (also known as a Rama-
chandran plot)was developed from modeling
C. Peptide nomenclature
studies of small peptides. However, the con-
Peptide chains have a direction and therefore formations of most of the amino acids in pro-
two different ends. The amino terminus (N teins are also located in the permitted areas.
terminus) ofa peptidehas a freeammonium The corresponding data for the small protein,
group, while the carboxy terminus (Ctermi- insulin (see p. 76), are represented by black
nus) is formed by the carboxylate group of the dots in 1.
last amino acid. In peptides and proteins, the
amino acid components are usually linked in
linear fashion. To express the sequence of a
peptide, it is therefore suf cient to combine
the three-letter or single-letter abbreviations
for the amino acid residues (see p. 60). This
sequence always starts at the N terminus. For
Koolman, Color Atlas of Biochemistry, 2nd edition © 2005 Thieme
All rights reserved. Usage subject to terms and conditions of license.
