BIOCHEMISTRY (I)

LIFS2210

Protein Structure (II)

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The four levels of protein structure

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-helix

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 Hidrogen bond

 Strands and  Sheets

•  Strands - polypeptide chains that are

almost fully extended
•  Sheets - multiple  strands arranged
side-by-side
•  Strands are stabilized by hydrogen bonds
between C=O and -NH on adjacent strands

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 Loops and Turns
• Loops and turns connect -helices and
-strands and allow a peptide chain to fold back on itself to make a
compact structure
• Loops - often contain hydrophilic residues and are found on protein
surfaces
• Turns - loops containing 5 residues or less

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The four levels of protein structure

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 1. Tertiary Structure of Proteins

• Tertiary structure describes the shape

of the fully folded polypeptide chain

• Tertiary structure results from the

folding of a polypeptide chain into a
closely-packed three-dimensional
structure

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 Examples of tertiary structure

Myoglobin

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 Tertiary Structure of Proteins

• Amino acids far apart in

the primary structure may
be brought together
• Stabilized primarily by
noncovalent interactions
(e.g. hydrophobic effects)
between side chains
• Disulfide bridges are also
part of tertiary structure

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Example of tertiary structure

Globular proteins Myoglobin

 Have compact,
spherical shapes.
 Carry out synthesis,
transport, and
metabolism in the
cells.
 Such as myoglobin
store and transport
oxygen in muscle.

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 2. Quaternary structure

• In proteins containing more than one polypeptide

chain, the spatial arrangements of those chains
(subunits) and the nature of contacts among them.

Hemoglobin

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 Quaternary structure

• Subunits (may be identical or different) have a

defined stoichiometry and arrangement
• Subunits are held together by many weak,
noncovalent interactions (hydrophobic,
electrostatic etc.)

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Quaternary Structure
The quaternary structure Hemoglobin
 Is the combination of two or
more tertiary units.
 Is stabilized by the same
interactions found in tertiary
structures.
 Of hemoglobin consists of two
alpha chains and two beta
chains. The heme group in
each subunit picks up oxygen
for transport in the blood to the
tissues.
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Summary of Protein Structures

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 3. Two major classes of proteins

• Fibrous proteins are structural proteins.

• Globular proteins perform most of the

chemical "work" of the cell - synthesis,
transport, and catabolism.

• Globular proteins are folded into compact

structures very unlike the extended,
filamentous forms of the fibrous proteins.
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Collagen Myoglobin

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 Fibrous proteins

• Provide mechanical support

• Often assembled into large cables or threads
• -Keratins: major components of hair and
nails
• Collagen: major component of tendons, skin,
bones and teeth

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 Collagen, a Fibrous Protein

• Collagen is a major protein in connective tissue of

vertebrates (25-35% of total protein in mammals)
• Diverse forms include tendons (ropelike fibers) and
skin (loosely woven fibers)
• Collagen consists of three left-handed helical chains
coiled around each other in a right-handed supercoil
• Three amino acids per turn, rise 0.31 nm per residue
(collagen is more extended than an  helix)

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Collagen triple helix

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 Interchain H bonding in collagen

• For each -Gly-X-Y-

triplet, one
interchain H bond
forms between
amide H of Gly in
one chain and
-C=O of residue X
in an adjacent
chain

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 Globular proteins
Three-dimensional folding of the protein myoglobin

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 Globular proteins

• Usually water soluble, compact, roughly

spherical
• Hydrophobic interior, hydrophilic surface
•  sheets are usually twisted, or wrapped into
barrel structures
• Globular proteins include enzymes and
regulatory proteins

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Type structures of globular proteins

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 Distribution of hydrophilic and hydrophobic
residues in a globular protein - cytochrome c

Red: hydrophorbic residues Green: hydrophilic residues

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4. In vivo Protein Folding and Stability

• Folding is a thermodynamically favored process

• Proteins are thought to fold “cooperatively” … the

first few interactions assist subsequent alignment
and folding

• The backbone is rearranged to achieve a stable

native conformation
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 Protein Folding Is Assisted by Chaperones

• Molecular chaperones increase rate of correct

folding and prevent the formation of incorrectly
folded intermediates
• Chaperones can bind to unassembled protein
subunits to prevent incorrect aggregation before
they are assembled into a multisubunit protein
• Most chaperones are heat shock proteins
(synthesized as temperature increases)
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 Chaperonin-assisted protein folding

• Hydrolysis of several ATP molecules is required

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 GroEL-GroES chaperonin

•Core consists of 2
identical rings
(7 GroE subunits in
each ring)
•Protein folding
takes place inside
the central cavity

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5. Protein Denaturation and Renaturation

• Denaturation - disruption of native conformation

of a protein, with loss of biological activity
• Energy required is small, perhaps only equivalent
to 3-4 hydrogen bonds
• Proteins denatured by heating or chemicals
• Some proteins can be refolded or renatured

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Applications of Denaturation
Denaturation of protein occurs
when
 An egg is cooked.
 The skin is wiped with
alcohol.
 Heat is used to cauterize
blood vessels.
 Instruments are sterilized in
autoclaves.

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Denaturation

Denaturation involves
 The disruption of bonds in the secondary, tertiary
and quaternary protein structures.
 Heat and organic compounds that break apart H
bonds and disrupt hydrophobic interactions.
 Acids and bases that break H bonds between polar
R groups and disrupt ionic bonds.
 Heavy metal ions that react with S-S bonds to form
solids.
 Agitation such as whipping that stretches peptide
chains until bonds break.
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Thermal denaturation of ribonuclease A

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• Heat denaturation
of ribonuclease
• Unfolding monitored
by changes in
ultraviolet (blue),
viscosity (red),
optical rotation
(green)

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Denaturation and renaturation of
ribonuclease A

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 Factors Determining Secondary and
Tertiary Structure

• Amino acid sequence

• Thermodynamic factors - Folding is a
thermodynamically favored process.
• Disulfide bonds - help to stabilize structure
once it has folded.
• Noncovalent bonding forces
– Charge-charge interaction
– Hydrogen bonds
– Van der Waals forces
– Hydrophobic interactions
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