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
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Figure 3–6 Four representations
describing the structure of a small
protein domain. Constructed from a string
of 100 amino acids, the SH2 domain is part
of many different proteins (see, for example,
Figure 3–61). Here, the structure of the
SH2 domain is displayed as (A) a
polypeptide backbone model, (B) a ribbon
model, (C) a wire model that includes the
amino acid side chains, and (D) a spacefilling
model (Movie 3.1). These images
are colored in a way that allows the
polypeptide chain to be followed from its
N-terminus (purple) to its C-terminus (red)
(PDB code: 1SHA).
Proteins come in a wide variety of shapes, and most are between 50 and
2000 amino acids long. Large proteins usually consist of several distinct protein
domains—structural units that fold more or less independently of each other, as
we discuss below. The structure of even a small domain is complex, and for clarity,
several different representations are conventionally used, each of which emphasizes
distinct features. As an example, Figure 3–6 presents four representations
of a protein domain called MBoC6 SH2, n3.101/3.06 a structure present in many different proteins in
eukaryotic cells and involved in cell signaling (see Figure 15–46).
Descriptions of protein structures are aided by the fact that proteins are built
up from combinations of several common structural motifs, as we discuss next.
The α Helix and the β Sheet Are Common Folding Patterns
When we compare the three-dimensional structures of many different protein
molecules, it becomes clear that, although the overall conformation of each protein
is unique, two regular folding patterns are often found within them. Both patterns
were discovered more than 60 years ago from studies of hair and silk. The
first folding pattern to be discovered, called the α helix, was found in the protein
α-keratin, which is abundant in skin and its derivatives—such as hair, nails, and
horns. Within a year of the discovery of the α helix, a second folded structure,
called a β sheet, was found in the protein fibroin, the major constituent of silk.
These two patterns are particularly common because they result from hydrogen-bonding
between the N–H and C=O groups in the polypeptide backbone,
without involving the side chains of the amino acids. Thus, although incompatible
with some amino acid side chains, many different amino acid sequences can form
them. In each case, the protein chain adopts a regular, repeating conformation.
Figure 3–7 illustrates the detailed structures of these two important conformations,
which in ribbon models of proteins are represented by a helical ribbon and
by a set of aligned arrows, respectively.