Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

THE SHAPE AND STRUCTURE OF PROTEINS
111
(A)
amino acid
(B)
+180
O
H
H
C
C α
N
H
R 2
C α
N H C
C α
phi psi
R
H
O
1 R 3
psi 0
peptide bonds
Figure 3–3 Steric limitations on the bond angles in a polypeptide
chain. (A) Each amino acid contributes three bonds (red) to the backbone
of the chain. The peptide bond is planar (gray shading) and does not permit
rotation. By contrast, rotation can occur about the C α –C bond, whose
angle of rotation is called psi (ψ), and about the N–C α bond, whose angle of
rotation is called phi (ϕ). By convention, an R group is often used to denote
an amino acid side chain (purple circles). (B) The conformation of the mainchain
atoms in a protein is determined by one pair of ϕ and ψ angles for each
amino acid; because of steric collisions between atoms within each amino
acid, most of the possible pairs of ϕ and ψ angles do not occur. In this socalled
Ramachandran plot, each dot represents an observed pair of angles in
a protein. The three differently shaded clusters of dots reflect three different
“secondary structures” repeatedly found in proteins, as will be described in
the text. (B, from J. Richardson, Adv. Prot. Chem. 34:174–175, 1981.
© Academic Press.)
–180
–180 0
phi
+180
beta sheet
left-handed
helix
alpha helix
(right-handed)
MBoC6 m3.03b/3.
MBoC6 m3.03/3.03
A fourth weak force—a hydrophobic clustering force—also has a central role
in determining the shape of a protein. 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 Panel 2–2,
pp. 92–93). Therefore, an important factor governing the folding of any protein is
glutamic acid
N
H
H
C
O
C
electrostatic
attractions
+
R
CH 2
CH 2
CH 2
O
C
H
H
O
N
+
H
CH 2
CH 2
van der Waals attractions
hydrogen bonds
O
C
R
H
C
C
H
O
H
N
C
O
C
H
N
R
H
C
C
O
CH 2
H
C
N
H
lysine
CH3 CH 3
H C O
C
CH 3
CH C 3
H
H
H
C CH N
3
N
H C H
C
C C N O
H
O
H
valine
alanine
valine
Figure 3–4 Three types of noncovalent bonds help proteins fold. Although a single one of these bonds is quite weak, many
of them act together to create a strong bonding arrangement, as in the example shown. As in the previous figure, R is used as a
general designation for an amino acid side chain.