Chapter 3
• Protein Structure
The SH2 domain
SEQUENCE DETERMINES STRUCTURE
Levels of protein structure
PRIMARY STRUCTURE
A peptide bond
The requirement that no two atoms overlap limits greatly the possible bond
angles in a polypeptide chain
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. Rotation
can occur about the Ca-C bond, whose angle of rotation
is called psi (y), and about the N-Ca bond, whose angle
of rotation is called phi (f)
The conformation of the main-chain atoms in a protein
is determined by one pair of f and y angles for each
acid. Because of steric collisions between atoms within
each amino acid, most pairs of f and y angles do not
occur. Each dot, in the Ramachandran plot shown here,
represents an observed pair of angles in a protein. In
a-helices, the backbone dihedral angles, f and y have
repeating values of -60°and -40° respectively.
some proteins containing proline.
SECONDARY STRUCTURE
The a helix is one of the major elements of secondary structure in proteins.
Main-chain N and O atoms are hydrogen-bonded to each other within a helices. (a) Idealized diagram of the path of the
main chain in an a helix. Alpha helices are frequently illustrated in this way. There are 3.6 residues per turn in an a helix,
which corresponds to 5.4 angstrom (1.5 angstrom per residue). (b) The same as (a) but with approximate positions for
main-chain atoms and hydrogen bonds included. The arrow denotes the direction from the N-terminus to the C-terminus.
(c) Schematic diagram of an a helix. Oxygen atoms are red, and N atoms are blue. Hydrogen bonds between O and N are
red and striated. The side chains are represented as purple circles.
The α-helix. The NH of every peptide bond is hydrogen-bonded to the CO of
a neighboring peptide bond located four peptide bonds away in the same
chain
The b-sheet. The individual peptide chains (strands) in a b-sheet are held
together by hydrogen-bonding between peptide bonds in different strands
The structure of a coiled-coil
TERTIARY STRUCTURE
Proteins fold into a conformation of lowest energy
Three types of noncovalent bonds that help proteins fold
A protein folds into a compact conformation
Hydrogen bonds in a protein molecule
A protein domain is a fundamental unit of organization
domains - structural units that fold more or less
independently of each other
The Src protein
The Src protein
Ribbon models of three different protein domains
PROTEIN FOLDING
How does a protein chain achieves its native conformation?
As an example, E. coli cells can make a complete, biologically active
protein containing 100 amino acids in about 5 sec at 37°C.
If we assume that each of the amino acid residues could take up 10
different conformations on average, there will be 10100 different
conformations for this polypeptide.
If the protein folds spontaneously by a random process in which it
tries all possible conformations before reaching its native state, and
each conformation is sampled in the shortest possible time (~10-13 sec),
it would take about 1077 years to sample all possible conformations.
There are two possible models to explain protein folding:
In the first model, the folding process is viewed as hierarchical, in which
secondary structures form first, followed by longer-range interactions to
form stable supersecondary structures. The process continues until
complete folding is achieved.
In the second model, folding is initiated by a spontaneous collapse of the
polypeptide into a compact state, mediated by hydrophobic interactions
among non-polar residues. The collapsed state is often referred to as the
‘molten globule’ and it may have a high content of secondary structures.
Most proteins fold by a process that incorporates features of both models.
Thermodynamically, protein folding can be viewed as a free-energy funnel
- the unfolded states are characterized by a high degree of conformational
entropy and relatively high free energy
- as folding proceeds, narrowing of the funnel represents a decrease in the
number of conformational species present (decrease in entropy) and
decreased free energy
Schematic pictures of a statistical ensemble of proteins
embedded in a folding funnel for a monomeric l repressor domain. At the top, the protein is in its
denatured state and thus fluctuating wildly, where both
energy and entropy are the largest. In the middle, the
transition state forms a minicore made of helices 4 and
5 and a central region of helix 1 drawn in the right half,
whereas the rest of protein is still denatured. At the
bottom is the native structure with the lowest energy and
entropy.
Takada, Shoji (1999) Proc. Natl. Acad. Sci. USA 96, 11698-11700
A schematic energy landscape for protein folding
Nature 426:885
Steps in the creation of a functional protein
The co-translational folding of a protein
The structure of a molten globule – a molten globule form of
cytochrome b562
Molecular chaperones help guide the folding of many proteins
A current view of protein folding
A unified view of some of the structures that
can be formed by polypeptide chains
Nature 426: 888
The hsp70 family of molecular chaperones. These proteins act early,
recognizing a small stretch of hydrophobic amino acids on a protein’s
surface.
The hsp60-like proteins form a large barrel-shaped structure that acts
later in a protein’s life, after it has been fully synthesized
Nature 379:420-426 (1996)
Cellular mechanisms monitor protein quality after protein synthesis
Exposed hydrophobic regions provide critical signals for protein quality control
The ubiquitin-proteasome pathway
Nature 426: 897
The proteasome
Processive cleavage of proteins
Processive protein digestion by the proteasome
Figure 6-90 Molecular Biology of the Cell (© Garland Science 2008)
The 19S cap – a hexameric protein unfoldase
Figure 6-91a Molecular Biology of the Cell (© Garland Science 2008)
Model for the ATP-dependent unfoldase activity of AAA proteins
Figure 6-91b Molecular Biology of the Cell (© Garland Science 2008)
Ubiquitin – a relatively small protein (76 amino acids)
Abnormally folded proteins can aggregate to cause destructive
human diseases
(C)
Cross-beta filament, a common type of protease-resistant protein
aggregate
(D)
A model for the conversion of PrP to PrP*, showing the likely
change of two α-helices into four β-strands
Regulation of protein folding in the ER
Nature 426: 886
A schematic representation of the general mechanism of
aggregation to form amyloid fibrils.
Nature 426: 887
Proteins can be classified into many families – each family member
having an amino acid sequence and a three-dimensional structure
that resemble those of the other family members
The conformation of two serine proteases
A comparison of DNA-binding domains (homeodomains) of the yeast
α2 protein (green) and the Drosophila engrailed protein (red)
Sequence homology searches can identify close relatives
The first 50 amino acids of the SH2 domain of 100 amino acids compared for
the human and Drosophila Src protein
Multiple domains and domain shuffling in proteins
Domain shuffling
An extensive shuffling of blocks of protein sequence (protein domains)
has occurred during protein evolution
A subset of protein domains, so-called protein modules, are generally
somewhat smaller (40-200 amino acids) than an average domain
(40-350 amino acids)
Each module has a stable core structure formed from strands of β sheet and
they can be integrated with ease into other proteins
Fibronectin with four fibronectin type 3 modules
Relative frequencies of three protein domains
Figure 3-18 Molecular Biology of the Cell (© Garland Science 2008)
Domain structure of a group of evolutionarily related proteins
that have a similar function – additional domains in
more complex organisms
Figure 3-19 Molecular Biology of the Cell (© Garland Science 2008)
Quaternary structure
Larger protein molecules often contain more than one polypeptide chain
Lambda cro repressor showing “head-to-head” arrangement
of identical subunits
DNA-binding site for the Cro dimer
ATCGCGAT
TAGCGCTA
The “head-to-tail” arrangement of four identical subunits that form
a closed ring in neuraminidase
HEMOGLOBIN
A symmetric assembly of two different subunits
A collection of protein molecules, shown at the same scale
Some proteins form long helical filaments
Protein Assemblies
Helical arrangement of actin molecules in an actin filament
Helices occur commonly in biological structures
A protein molecule can have an elongated, fibrous shape
Collagen
Elastin polypeptide chains are cross-linked together to form rubberlike,
elastic fibers
Extracellular proteins are often stabilized by covalent cross-linkages
Disulfide bonds
Proteolytic cleavage in insulin assembly