Protein Tertiary Structure
What to Know
• What are some protein functions?
• General principles for protein folding
• General structural features of globular and structural
proteins
• Know the 4 common globular protein motifs
• Understand how protein structures are stabilized and why
some portions of proteins are marginally stable
• Why is protein flexibility and motion important?
TERTIARY STRUCTURE OF PROTEINS
• THE THREE-DIMENSIONAL CONFORMATION
OF A PROTEIN
• The overall spatial relationships between
segments of primary and secondary
structure
• The scope of tertiary structure is thus
long-range
• Determined by x-ray diffraction and NMR
Globular Protein Functions
 Functionally this group is most diverse:
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Enzymes
Transport proteins
Antibodies
Cell surface proteins
Integral membrane proteins
Virus coat proteins
Storage proteins
DNA binding proteins
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How Do Polypeptides Fold into Three-Dimensional Protein
Structures?
Several important principles:
• Secondary structures form wherever possible (due to
formation of large numbers of H bonds)
• Helices and sheets often pack close together
• Peptide segments between secondary structures tend to be
short and direct
• Proteins fold so as to form the most stable structures.
Stability arises from:
– Formation of large numbers of intramolecular hydrogen
bonds
– Reduction in the surface area accessible to solvent that
occurs upon folding
How Do Polypeptides Fold into Three-Dimensional
Protein Structures?
• Two factors lie at the heart of these principles:
– Proteins are typically a mixture of hydrophilic
and hydrophobic amino acids
– The hydrophobic groups tend to cluster
together in the folded interior of the protein
Tertiary Structure
Several important principles:
Proteins fold to make the most stable structures.
Globular proteins. Create maximum internal
bonds and minimize solvent contact.
Fibrous proteins. Create maximum intermolecular
bonds and maximize molecule to molecule
contact.
FIBROUS PROTEINS
• Characterized by association of helical chains
which coil around each other forming coiledcoils.
• Keratin and Myosin (heptad repeat)
• Collagen (triplet repeat, G-X-Y, G-P-P)
Structure
of Collagen
• Triple helical structure:
●Three α chains each
coiled in left-handed
sense (Minor helix).
●Three α Chains coiled
about each other
in right-handed
sense (Major helix).
H-bonds in the collagen fold
From Gly-N groups to C=O function of the preceding amino acid
in a neighboring chain. Also, hydroxyproline participates.
Globular Proteins
• Most polar residues face the outside of the protein
and interact with solvent
• Most hydrophobic residues face the interior of the
protein and interact with each other
• Packing of residues is close
• However, ratio of VdW volume to total volume is only
0.72 to 0.77, so empty space exists
• The empty space is in the form of small
cavities"Random coil" is not random
• Structures of globular proteins are not static
• Various elements and domains of protein move to
different degrees
• Some segments of proteins are very flexible and
disordered
Most Globular Proteins Belong to One of Four
Structural Classes
• Proteins can be classified according to the
type and arrangement of secondary structure
• There are four classes:
– All α proteins, in which α helices predominate
– All β proteins, in which β sheets predominate
– α/β proteins, in which helices and sheets are
intermingled
– α+β proteins, which contain separate α-helical
and β-sheet domains
The Serine Proteases
Trypsin, chymotrypsin, elastase, thrombin, subtilisin,
plasmin, TPA
• All involve a serine in catalysis - thus the name
• Ser is part of a "catalytic triad" of Ser, His, Asp
• Serine proteases are homologous, but locations of
the three crucial residues differ somewhat
• Enzymologists agree, however, to number them
always as His-57, Asp-102, Ser-195
Comparison of the amino acid
sequences of chymotrypsinogen,
trypsinogen, and elastase.
Filled circles indicate residues that
are identical in all three proteins.
The positions of the three
catalytically important active-site
residues (His57, Asp102, and Ser195)
are indicated.
Structure of chymotrypsin (white) in a complex
with eglin C (blue ribbon structure), a target
protein.
The residues of the catalytic triad (His57, Asp102,
and Ser195) are highlighted. His57 (blue) is
flanked above by Asp102 (red) and on the right
by Ser195 (yellow).
Catalytic site is filled by a peptide segment of
eglin. Note how close Ser195 is to the peptide
that would be cleaved in a chymotrypsin
reaction.
Calcium Binding Motif
Parvalbumin
Bob Kretsinger
Globular Proteins
The structure of ribonuclease, showing elements of helix, sheet
and random coil.
Protein surfaces are complex
The surfaces of proteins are
complementary to the
molecules they bind.
Waters on the Protein Surface Stabilize the Structure
The surfaces of proteins
are ideally suited to form
multiple H bonds with
water molecules.
Alpha Structures
Coiled Coils: More stable than single helix or two straight rod-like helices
Francis Crick
Salt bridges can also stabilize coiled coils
Four helix bundle is common in domain structure proteins
Myohemerythrin, cytichrome c’,ferritin, coat protein of TMV
Beta Structures
Alpha/beta Structures
Beta-alpha-beta proteins: triosphosphate isomerase and co-enzyme binding
domain of a dehydrogenase: beta stands are parallel
Methylmalonyl-coenzyme A mutase
Inside of the barrel is lined with hydrophillic side
chains (S and T) which creates a hole for substrate to
bind
Examples of Open twisted
α/β structures: Flavodoxin
and adenylate kinase
Denaturation Leads to Loss of Protein Structure and
Function
• The cellular environment is suited to maintaining the
weak forces that preserve protein structure and
function
• External stresses – heat, chemical treatment, etc. –
can disrupt these forces in a process termed
denaturation – the loss of structure and function
• The cooking of an egg is an everyday example
• Ovalbumin, the principal protein in egg white,
remains in its native structure up to a characteristic
melting temperature, Tm determined via differential
scanning calorimetry (DSC)
• Above this temperature, the structure unfolds and
function is lost
Denaturation Leads to Loss of Protein
Structure and Function
The proteins of egg white are denatured during cooking. More
than half of the protein in egg white is ovalbumin.
Marginal Stability of the Tertiary Structure
Makes Proteins Flexible
• A typical folded protein is only marginally
stable
• It is logical to think that stability is important
to function, so why are proteins often only
marginally stable?
• The answer appears to lie in flexibility and
motion
• It is becoming increasingly clear that
flexibility and motion are important to
protein function
Motion is Important for Globular Proteins
• Protein are dynamic structures – they
oscillate and fluctuate continuously about
their average or equilibrium structures
• This flexibility is essential for protein
functions, including:
– Ligand binding
– Enzyme catalysis
– Enzyme regulation
Motion is Important for Globular Proteins
Proteins are dynamic
structures. The
marginal stability of a
tertiary structure leads
to flexibility and motion
in the protein.
Some Proteins Are Intrinsically Unstructured
Intrinsically unstructured proteins (IUPs) contact their target
proteins over a large surface area.
Diseases of Protein Folding