BIOC 2162

Circulatory and Secretory Systems

 Course Content
• Protein Stability and Folding
• Protein Sorting and Transport
• Intracellular Vesicular Traffic
• The Cytoskeleton
• Hormones
• Plant Hormones
• Respiratory Systems
• Circulatory Systems
 Recommended Reading
• Alberts: Molecular Biology of the Cell

• Lehninger: Principles of Biochemistry

• Stryer: Biochemistry

• Brandon and Tooze : Introduction to Protein Structure

• Fersht: Structure and Mechanism in Protein Science

 Course Evaluation
• Final Exam 50%

• 2 Incourse Examinations 10% Each

• 15% Dr. Lennon (Tutorial Worksheets and

Quizes)

• 15% Dr. Bowrin

Protein Folding

Protein Structure
Levels of Protein Structure
 The Alpha Helix
• The a helical conformation was proposed in 1950 by Pauling
and Corey, with Max Perutz providing supporting evidence
fro the X ray diffraction of a-keratin.

• The simplest arrangement of the polypeptide chain can

assume with its rigid peptide bonds is the a helix.

• In this structure the polypeptide backbone is tightly wound

around an imaginary axis drawn longitudinally through the
middle of the helix and the R groups of the amino acid
residues protruding outward from the helix.
 The repeating unit is a single
turn of the helix which extends
about 5.4 Å along the long axis
(3.6 residues).

the a helix found in all proteins is right handed

 
• The helix forms readily due to an optimal use of internal
hydrogen bonding.

• The structure is stabilized by a hydrogen bond between the

hydrogen atom attached to the electronegative nitrogen
atom of a peptide bond and the carbonyl oxygen atom of
the 4th amino acid on the amino-terminal side of the
peptide bond.

• Therefore within the helix every peptide bond (except

those close to the end of the helix) participates in hydrogen
bonding. All of these hydrogen bonds give the helix
considerable stability.
Not all polypeptides can form a stable a helix
• Interactions between amino acid side chains can stabilize or destabilize the
structure.

• Long stretches of negative or positive charges will repel each other that
formation of the helix is prevented (e.g. Glu or Lys/Arg)

• Large bulky side chains next to each other can result is steric interference and
again stop the formation of the helical structure.

• Oppositely charged amino acids are often found 3 or 4 residues apart.

• The twist of the helix allows these side chains to intact and allowing the
formation of an ion pair. Hydrophobic side chains are often found similarly
spaced to allow hydrophobic interactions. Both of these interactions provide
stability to the a helix.
Glycine and Alanine

Bad Good
• In proline the nitrogen atom is part of a rigid
ring therefore rotation about the N-Ca bond is
not possible. Proline introduces a destabilizing
kink in a a helix.
• Also the nitrogen in proline is unable to
hydrogen bond, for these reasons proline is
rarely found in a helices.
 Dipoles

All peptide bonds have a dipole moment pointing in

the same direction.

Therefore there is a dipole moment across the whole helix

increasing with helix length
 Ends of Helices
• The four amino acids at the end of the helix do not
fully hydrogen bond.

• Negatively charged residues are found at near the

amino terminal where they interact with the positive
charge of the helix, stabilizing the structure.

• Positively charged residues are found at the carboxyl

end where they stabilize the negative end of the helix’s
dipole.
The b Sheet
β - turns involve four amino acid residues with a hydrogen bond between
the C=O group of the first residue and the N–H group of the fourth
 Loops

As much as one third of the amino acid residues in a typical protein

are found in such non repetitive structures. Loops often contain
hydrophilic residues and are usually found on the surfaces of
proteins, some loops can consist of many residues of extended
non repetitive structure.
 Tertiary Structure
• Tertiary structure results from the folding of a polypeptide into a closely
packed three-dimensional structure.

• An important feature of tertiary structure is that amino acids residues that

are far apart in the primary structure are brought together, permitting
interactions among their side chains.

• Whereas secondary structure is stabilized by hydrogen bonding between

amide hydrogens and carbonyl oxygens of the polypeptide backbone,
tertiary structure is stabilized primarily by noncovalent interactions
between the side chains of amino acid residues.

• Disulphide bonds though covalent are also elements of tertiary structure.

A. Super-secondary structure (Motifs)
Larger motifs are often called domain folds
because they make up the core of a domain.
C-terminal WD40 domain
of Tup1, a transcriptional
co-repressor in yeast,
which adopts a 7-bladed
beta-propeller fold
Domains

Example of a Protein
with 3 domains
(Pyruvate Kinase)

Each domain forms a compact

three-dimensional structure and
often can be independently stable
and folded.
 Domain Size
• The size of individual structural domains varies from
36 residues in E-selectin to 692 residues in
lipoxygenase-1, but the majority, 90%, have less than
200 residues with an average of approximately 100
residues.

• Very short domains, less than 40 residues, are often

stabilised by metal ions or disulfide bonds. Larger
domains, greater than 300 residues, are likely to
consist of multiple hydrophobic cores.
 Lactate and Malate Dehydrogenase

Some proteins share domains indicating a

common evolutionary decent
 One commonly used classification scheme
groups domains into four categories
• The all a-category contains domains that
consist of entirely a helices and loops

• All b domains contain only b sheets and non

repetitive structures that link the b strands
 One commonly used classification scheme
groups domains into four categories
• The other two categories contain domains that have a
mixture of a helices and b strands

• Domains in the a/b class have supersecondary structures

such as the bab motif and others in which regions of a helix
and b strand alternate in the polypeptide chain

• In the a + b category the domains consist of local clusters of

a helices and b sheet where each type of secondary
structure arises from separate contiguous regions of the
polypeptide chain
 Why Quaternary Structure?
• Oligomers are usually more stable than their
dissociated subunits, suggesting the
quaternary structure prolongs the life of a
protein in vivo

• The active sites of some oligomeric enzymes

are formed by residues from adjacent
polypeptide chains
 Why Quaternary Structure?
• The three-dimensional structures of many
oligomeric proteins change when the proteins
bind ligands.

• Both the tertiary and quaternary structures may

be altered.

• Such changes are key elements in the regulation

of biological activity of certain oligomeric proteins
 Why Quaternary Structure?
• Different proteins can share the same subunits.

• Since many subunits have a defined function evolution

has favoured selection for different combinations of
subunits to carry out related functions.

• This is more efficient than selection for an entirely

new monomeric protein that duplicates part of the
function
E.g. The L protein of the mitochondrial
glycine cleavage system

The L protein, dihydrolipoamide dehydrogenase,

is also a component of the pyruvate
dehydrogenase complex, the alpha-ketoglutarate
dehydrogenase complex, and the branched-chain
alpha-keto acid dehydrogenase complex. It is also
found in plant mitochondrial glycine
decarboxylase complex coupled to serine
hydroxymethyltransferase